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Protein Structure Comparison by Alignment of Distance Matrices
Abstract
With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.
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“The templates were pairwise structurally aligned according to DALILite (41,42), using HIF-2 α as a reference. The sequence alignments were obtained by CLUSTALW (43), and the result was confirmed using the Align-2D command within the MODELLER program (37-39).”
From Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis (2007) · cites this paper as [41]
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Structure and Mechanism of Helicobacter pylori Fucosyltransferase
Sun, H., Lin, S., Ko, T., et al. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m610285200 · Cited by 137
Structure of a Multifunctional Protein
Yoder, M. D., Thomas, L. M., Tremblay, J. M., Oliver, R. L., Yarbrough, L. R., & Helmkamp, G. M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m010131200 · Cited by 137
Schneider, T. R. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444901019291 · Cited by 137
“A generalization of the algorithm for cases where closely homologeous structures are compared and a robust mapping of corresponding atoms in three dimensions can be achieved using existing methods such as DALI (Holm & Sander, 1993), which is also based on difference distance matrices, is a mostly technical problem [fo…”
MethodProtein structure comparison using iterated double dynamic programming
Taylor, W. R. (1999) · Protein Science · doi:10.1110/ps.8.3.654 · Cited by 139
“…structures maintain a linear equivalence and while this is usually a firm basis for postulating evolutionary relationship, other methods can identify similarity without this constraint~Nussinov & Wolfson, 1991; Holm & Sander, 1993; Grindley et al., 1993; Artymiuk et al., 1994; Gibrat et al., 1997!.”
MethodSwiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.
Herzberg, O., Chen, C. C., Kapadia, G. G., et al. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.7.2652 · Cited by 137
Wang, W., Kim, R., Jancarik, J., et al. (2001) · Structure · doi:10.1016/s0969-2126(00)00558-x · Cited by 137
Discrimination of thermophilic and mesophilic proteins
Taylor, T. J., & Vaisman, I. I. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-s1-s5 · Cited by 138
“The members of these non-redundant sets of chains from thermophilic organisms were each then submitted to structure comparison and alignment servers (CE[66] , SSM [67], DALI [68], VAST [69]) to obtain mesophilic structure neighbors with rmsd no greater than about 4 Å with respect to the thermophile where the structura…”
BackgroundCrystal Structure and Activity of Human p23, a Heat Shock Protein 90 Co-chaperone
Weaver, A. J., Sullivan, W. P., Felts, S. J., Owen, B. A. L., & Toft, D. O. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m003410200 · Cited by 136
Solution Structure of Human Cofilin
Pope, B. J., Zierler-Gould, K. M., Kühne, R., Weeds, A. G., & Ball, L. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310148200 · Cited by 135
Guerin, M. E., Korduláková, J., Schaeffer, F., Svetlíková, Z., Buschiazzo, A., Giganti, D. O., Gicquel, B., Mikušová, K., Jackson, M., & Alzari, P. M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702087200 · Cited by 135
Liu, Z., Macías, M. J., Bottomley, M., Stier, G., Linge, J. P., Nilges, M., Bork, P., & Sattler, M. (1999) · Structure · doi:10.1016/s0969-2126(00)88346-x · Cited by 137
“Searches in the Protein Data Bank For the searches in the PDB, coordinates of the lowest-energy waterrefined structure (residues 12‐90) of the Sgs1p HRDC domain were submitted to the Dali server at http://www2.ebi.ac.uk/dali [ 23 ].”
MethodSprague, E. R., Wang, C., Baker, D. A., & Björkman, P. J. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040148 · Cited by 136
“[29] identified the coxsackie virus and adenovirus receptor”
BackgroundCai, M., Huang, Y. K., Zheng, R., et al. (1998) · Nature Structural Biology · doi:10.1038/2345 · Cited by 136
“Searching of the Brookhaven protein structure database for structural similarity was carried out using the program DAL”
Methodvan Aalten, D. M. F., Dirusso, C., Knudsen, J., et al. (2000) · The EMBO Journal · doi:10.1093/emboj/19.19.5167 · Cited by 136
The structure of the conserved neurotrophic factors MANF and CDNF explains why they are bifunctional
Parkash, V., Lindholm, P., Peränen, J., Kalkkinen, N., Oksanen, E., Saarma, M., Leppänen, V., & Goldman, A. (2009) · Protein Engineering Design and Selection · doi:10.1093/protein/gzn080 · Cited by 136
“Comparison of CDNF-DC and MANF with other structures A DALI search (Holm and Sander, 1993) of the Protein Data Bank (PDB) showed that the CDNF-DC and MANF-N are structurally similar to SAPLIPs, as defined in the SCOP database (Murzin et al., 1995).”
MethodAlmeida, M. S., Cabral, K. M. D. S., Kurtenbach, E., Almeida, F. C. L., & Valente, A. P. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5252 · Cited by 136
Structural basis for the reversible activation of a Rho protein by the bacterial toxin SopE
Buchwald, G., Friebel, A., Galán, J. E., Hardt, W., Wittinghofer, A., & Scheffzek, K. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf329 · Cited by 135
“A homology search with the program DALI (Holm and Sander, 1993) did not identify similarity with the Rho family-speci®c DH domains from the eukaryotic RhoGEFs Sos, Trio, bPIX or Tiam1 (Aghazadeh et al.”
MethodStructural principles within the human-virus protein-protein interaction network
Franzosa, E. A., & Xia, Y. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1101440108 · Cited by 132
“…which the observed interface mimicry can be explained by structural and sequence mimicry, we measured the similarity at the structural level [Dali (26) z -score] and the sequence level [BLAST (27) E -value] between viral proteins and the human binding partners of their target proteins whose…”
BackgroundRoberts, D. L., Weix, D. J., Dahms, N. M., & Kim, J. P. (1998) · Cell · doi:10.1016/s0092-8674(00)81192-7 · Cited by 135
The FACT Spt16 “peptidase” domain is a histone H3–H4 binding module
Stuwe, T., Hothorn, M., Lejeune, E., Rybin, V., Bortfeld‐Miller, M., Scheffzek, K., & Ladurner, A. G. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712293105 · Cited by 135
“Structural homology searches return a bacterial prolidase and creatinase [Protein Data Bank ID codes 1CHM and 1PV9 (31, 32); DALI (55)”
BackgroundScoring profile‐to‐profile sequence alignments
Wang, G., & Dunbrack, R. L. (2004) · Protein Science · doi:10.1110/ps.03601504 · Cited by 135
“Alignment pairs were selected for the test set from the remaining pairs with the following criteria: (a) R (cid:1) 0.9 or (b) consensus structural alignment length ( N both is >100, and the alignment length difference between CE and DALI is 20% of the average length of the CE and DALI alignments.”
BackgroundMethodInfluentialThe crystal structures of two spermadhesins reveal the CUB domain fold
Romero, A., Romão, M. J., Varela, P. F., et al. (1997) · Nature Structural Biology · doi:10.1038/nsb1097-783 · Cited by 135
Hatanaka, H., Ogura, K., Moriyama, K., Ichikawa, S., Yahara, I., & Inagaki, F. (1996) · Cell · doi:10.1016/s0092-8674(00)81305-7 · Cited by 135
Svetlitchnaia, T., Svetlitchnyi, V., Meyer, O., & Dobbek, H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601420103 · Cited by 134
The structure of the ferric siderophore binding protein FhuD complexed with gallichrome.
Vogel, H. J., Tari, L. W., Clarke, T. E., Ku, S.-Y., & Dougan, D. R. (2000) · Nature Structural Biology · doi:10.1038/74048 · Cited by 134
Exploring the structure and function paradigm.
Redfern, O., Dessailly, B. H., & Orengo, C. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.05.007 · Cited by 133
“Significant global structural similarity can be used to transfer functional annotations where close homology can often be identified in the absence of high similarity at the sequence level, using methods such as CE [37], STRUCTAL [13], DALI [38], CATHEDRAL [14], FATCAT [39] and SSM [40].”
MethodZahn, R. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.09.048 · Cited by 134
Crystal structure of a clip‐domain serine protease and functional roles of the clip domains
Piao, S., Song, Y.-L., Kim, J. H., et al. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600891 · Cited by 134
“While the structure of the SPL domain of PPAF-II is similar to chymotrypsin-like proteases (Figure 2C), that of the clip domain is a new fold according to a database search using the program DALI (Holm and Sander, 1993).”
MethodCrystal Structure of Maltose Phosphorylase from Lactobacillus brevis
Egloff, M. P., Uppenberg, J., Haalck, L., & TILBEURGH, H. V. (2001) · Structure · doi:10.1016/s0969-2126(01)00626-8 · Cited by 135
Hayashi, I., Oyama, T., & Morikawa, K. (2001) · The EMBO Journal · doi:10.1093/emboj/20.8.1819 · Cited by 134
Evolution of protein sequences and structures
Wood, T. C., & Pearson, W. R. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2972 · Cited by 132
“The DALI structure comparison program also calculates a z-value to represent the signi®cance of a structural similarity (Holm & Sander, 1993).”
MethodSerre, L., Vallée, B., Bureaud, N., Schoentgen, F., & Zelwer, C. (1998) · Structure · doi:10.1016/s0969-2126(98)00126-9 · Cited by 132
Structural Insights into the Enzymatic Mechanism of the Pathogenic MAPK Phosphothreonine Lyase
Zhu, Y., Li, H., Long, C., Hu, L., Xu, H., Liu, L., Chen, S., Wang, D., & Shao, F. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.11.011 · Cited by 133
“No similar structures were retrieved from the DALI as well as the SSM server with the SpvC structure as the bait (Holm and Sander, 1993; Krissinel and Henrick, 2004).”
MethodKerr, I. D., Wadsworth, R. I. M., Cubeddu, L., et al. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg272 · Cited by 133
Anbanandam, A., Albarado, D. C., Nguyen, C. T. Y., Halder, G. A., Gao, X., & Veeraraghavan, S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607171103 · Cited by 136
Alpha-kinases: analysis of the family and comparison with conventional protein kinases
Drennan, D., & Ryazanov, A. G. (2003) · Progress in Biophysics and Molecular Biology · doi:10.1016/s0079-6107(03)00060-9 · Cited by 134
Lubkowski, J. T., Hennecke, F., Plückthun, A., et al. (1998) · Nature Structural Biology · doi:10.1038/nsb0298-140 · Cited by 133
Adinolfi, S. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.16.1865 · Cited by 133
“Modelling of the region 64–174 of Yfh1 (spanning the conserved globular domain) was based on a multiple sequence alignment calculated by CLUSTALX (45) and checked with a structural alignment achieved by Dali ( 46 ).”
MethodStructural Basis for a Munc13–1 Homodimer to Munc13–1/RIM Heterodimer Switch
Lu, J., Machius, M., Dulubova, I., Dai, H., Südhof, T. C., Tomchick, D. R., & Rizo, J. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040192 · Cited by 132
“A structural comparison using DALI [26] showed that, among C2 domains deposited in the Protein Data Bank (http://www.”
BackgroundInfluentialA Novel Copper-Binding Fold for the Periplasmic Copper Resistance Protein CusF,
Loftin, I. R., Franke, S., Roberts, S. A., Weichsel, A., Heroux, A., Montfort, W. R., Rensing, C., & McEvoy, M. M. (2005) · Biochemistry · doi:10.1021/bi050827b · Cited by 133
“atrosepticaSCRI1043 (YP_049490, residues 401 -485), (33)D.”
Fast protein tertiary structure retrieval based on global surface shape similarity
Sael, L., Li, B., La, D., Fang, Y., Karthik Ramani, A., Rustamov, R. M., & Kihara, D. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22030 · Cited by 132
Crystal Structure of the Dimeric C-terminal Domain of TonB Reveals a Novel Fold
Chang, C., Mooser, A., Plückthun, A., & Wlodawer, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m102778200 · Cited by 133
Treble clef finger--a functionally diverse zinc-binding structural motif
Grishin, N. V. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.8.1703 · Cited by 131
“Structure similarity searches against the Protein Data Bank (PDB) (14) maintained at the Research Collaboratory for Structural Bioinformatics were performed using DALI (15), VAST (16) and CE (17) programs with default parameters.”
MethodMeasuring the similarity of protein structures by means of the universal similarity metric
Krasnogor, N., & PELTA, D. A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth031 · Cited by 132
“…use is not forthcoming and a variety of structure comparison methods have been used in classification servers, such as SCOP (Murzin et al., 1995), DALI (Holm and Sander, 1993), LGA (Zemla, 2000, http://PredictionCenter.llnl.gov/local/lga; Zemla et al., 1999), CATH (Orengo et al., 1997) and others.”
BackgroundMethodInfluentialZinc-dependent dimers observed in crystals of human endostatin
Ding, Y., Javaherian, K., Lo, K.-M., Chopra, R., Boehm, T., Lanciotti, J., Harris, B. A., Li, Y., Shapiro, R., Hohenester, E., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.18.10443 · Cited by 130
Howard, B. R., Endrizzi, J. A., & Remington, S. J. (2000) · Biochemistry · doi:10.1021/bi992519h · Cited by 132
Graziewicz, M. A., Longley, M. J., Bienstock, R. J., Zeviani, M., & Copeland, W. C. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb805 · Cited by 131
“A structural alignment of solved family A polymerase X-ray crystal structures was done using DAL”
MethodSträter, N., Sherratt, D. J., & Colloms, S. D. (1999) · The EMBO Journal · doi:10.1093/emboj/18.16.4513 · Cited by 131
“(D) Stereo view of a superposition of the N-terminal domains of PepA (cyan) and LAP (orange) using the DALI server (Holm and Sander, 1993).”
MethodCrystal Structure of ClpX Molecular Chaperone from Helicobacter pylori
Kim, D. Y., & Kim, K. K. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305882200 · Cited by 131
Yamasaki, K., Kigawa, T., Inoue, M., Tateno, M., Yamasaki, T., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Tomo, Y., et al. (2004) · The Plant Cell · doi:10.1105/tpc.104.026112 · Cited by 130
“Structure of the B3 DNA Binding Domain 3455 (A) Structures of the EcoRII N-terminal domain (left) and RAV1-B3 (right) are viewed from the same orientation as aligned by the program DALI (Holm and Sander, 1993).”
BackgroundMethodInfluentialCrystal structure of human mitoNEET reveals distinct groups of iron–sulfur proteins
Lin, J., Zhou, T., Ye, K., & Wang, J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702426104 · Cited by 135
CLICK—topology-independent comparison of biomolecular 3D structures
Nguyen, M. N., Tan, K. P., & Madhusudhan, M. S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr393 · Cited by 130
“Over each of these datasets, the alignment accuracy of CLICK was compared with other popular protein structure alignment programs including MUSTANG (21), Geometric Hashing (C-alpha Match) (27–29), SALIGN (19), DALI (22,30) and alignments from the HOMSTRAD database (4).”
MethodCatalytic Promiscuity and the Divergent Evolution of DNA Repair Enzymes
O’Brien, P. (2006) · Chemical Reviews · doi:10.1021/cr040481v · Cited by 131
Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae
Sagermann, M., Stevens, T. H., & Matthews, B. W. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.131192798 · Cited by 130
Solution structure of the TAZ2 (CH3) domain of the transcriptional adaptor protein CBP
Guzman, R. N. D., Liu, H. Y., Martinez‐Yamout, M. A., Dyson, H. J., & Wright, P. E. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4141 · Cited by 135
Eijkelenboom, A. P. A. M., van den Ent, F. M. I., Vos, A., Doreleijers, J. F., Hård, K., Tullius, T. D., Plasterk, R. H. A., Kaptein, R., & Boelens, R. (1997) · Current Biology · doi:10.1016/s0960-9822(06)00332-0 · Cited by 128
“Possible structural similarity of IN1–55 to other proteins was investigated with the Dali Web server [37].”
Determination of protein function, evolution and interactions by structural genomics
Teichmann, S. A., Murzin, A. G., & Chothia, C. (2001) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00215-3 · Cited by 130
“Comparison of the structure of the protein product of gene MJ-0226 with those of other proteins [ 6 ] showed that it is structurally similar to the anticodon-binding domains of histidyl- and glycyl-tRNA synthetases and to nucleotide-binding domains of other proteins [3•].”
MethodResultBrown, G., Singer, A. U., Proudfoot, M., Skarina, T., Kim, Y., Chang, C., Dementieva, I., Kuznetsova, E., González, C. F., Joachimiak, A., et al. (2008) · Biochemistry · doi:10.1021/bi800097h · Cited by 125
“The search for structural homologues of YbaS using the DALI (53) (http://www.”
BackgroundInfluentialMartinez-Fleites, C., Proctor, M., Roberts, S. M., et al. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.09.005 · Cited by 129
Exhaustive Enumeration of Protein Domain Families
Heger, A., & Holm, L. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00269-9 · Cited by 130
Self-citationA novel RNA-binding motif in influenza A virus non-structural protein 1
Chien, C.-Y., Tejero, R., Huang, Y. J., Zimmerman, D. E., Ríos, C. B., Krug, R. M., & Montelione, G. T. (1997) · Nature Structural & Molecular Biology · doi:10.1038/nsb1197-891 · Cited by 129
The DCX-domain tandems of doublecortin and doublecortin-like kinase
Kim, M. H., Cierpicki, T., Derewenda, U., Krowarsch, D., Feng, Y., Devedjiev, Y. D., Dauter, Z., Walsh, C. A., Otlewski, J., Bushweller, J. H., et al. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb918 · Cited by 129
Comparative analysis of structural properties of the C‐type‐lectin‐like domain (CTLD)
Zelensky, A. N., & Gready, J. E. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10626 · Cited by 129
The structure of an actin-crosslinking domain from human fimbrin
Goldsmith, S. C., Pokala, N., Shen, W., et al. (1997) · Nature Structural Biology · doi:10.1038/nsb0997-708 · Cited by 128
Structural Basis for Interactions between Tenascins and Lectican C-Type Lectin Domains
Lundell, A., Olin, A. I., Mörgelin, M., al-Karadaghi, S., Aspberg, A., & Logan, D. T. (2004) · Structure · doi:10.1016/j.str.2004.05.021 · Cited by 127
Meinhart, A., Alonso, J. C., Sträter, N., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0434325100 · Cited by 127
Classification schemes for protein structure and function
Ouzounis, C. A., Coulson, R., Enright, A. J., Kunin, V., & Pereira‐Leal, J. B. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1113 · Cited by 126
Structure of the measles virus hemagglutinin
Colf, L. A., Juo, Z. S., & García, K. C. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1342 · Cited by 127
Synapsin I is structurally similar to ATP‐utilizing enzymes
Esser, L., Wang, C.-R., Hosaka, M., Smagula, C. S., Südhof, T. C., & Deisenhofer, J. (1998) · The EMBO Journal · doi:10.1093/emboj/17.4.977 · Cited by 127
“Surprisingly, the three-dimensional alignment (DALI; Holm and Sander, 1993) of synC with the structures deposited in the Brookhaven protein data bank (PDB; Bernstein et al., 1977) revealed strong architectural similarities to the following enzymes: glutathione synthetase (GSHase; Yamaguchi et al.,…”
MethodOlson, R., & Gouaux, E. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.045 · Cited by 127
Solution Structure of Human BCL-w
Denisov, A. Y., Murthy, M. S., Chen, G., Khadir, A., Beauparlant, P., Attardo, G., Shore, G. C., & Gehring, K. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m301798200 · Cited by 127
Pejchal, R., & Ludwig, M. L. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0030031 · Cited by 126
“In contrast, DALI searches that assess structural similarities [23] reveal that the N-terminal barrel is more similar to the C-terminal barrel of MetE than to any other known protein, suggesting that its immediate precursor is the Hcy barrel of MetE.”
BackgroundStructural insights into mechanism and specificity of O‐GlcNAc transferase
Clarke, A., Hurtado‐Guerrero, R., Pathak, S., Schüttelkopf, A. W., Borodkin, V. S., Shepherd, S. M., Ibrahim, A. F. M., & van Aalten, D. M. F. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.186 · Cited by 130
“However, struc- ture searches with DALI (Holm and Sander, 1993) reveals that CDI/II of XcOGT, and thus the GT41 family, in fact form a single catalytic domain of the GT-B fold frequently observed in GTs (Davies et al, 2005).”
BackgroundSolution Structure of the Chitin-binding Domain of Bacillus circulans WL-12 Chitinase A1
Ikegami, T., Okada, T., Hashimoto, M., Seino, S., Watanabe, T., & Shirakawa, M. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.18.13654 · Cited by 127
Loop Closure and Intersubunit Communication in Tryptophan Synthase,
Schneider, T. R., Gerhardt, E., Lee, M., Liang, P., Anderson, K. S., & Schlichting, I. (1998) · Biochemistry · doi:10.1021/bi9728957 · Cited by 126
Settembre, E. C., Dorrestein, P. C., Park, J.-H., et al. (2003) · Biochemistry · doi:10.1021/bi026916v · Cited by 126
A six-stranded double-psi β barrel is shared by several protein superfamilies
Castillo, R. M., Mizuguchi, K., Dhanaraj, V., Albert, A., Blundell, T. L., & Murzin, A. G. (1999) · Structure · doi:10.1016/s0969-2126(99)80028-8 · Cited by 126
“A database search with the program DALI [16] against the structure of ADC identified eight proteins that have statistically significant similarity scores.”
MethodMancheño, J. M., Tateno, H., Goldstein, I. J., Martínez-Ripoll, M., & Hermoso, J. A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m413933200 · Cited by 123
Rudenko, G., Nguyen, T., Chelliah, Y., Südhof, T. C., & Deisenhofer, J. (1999) · Cell · doi:10.1016/s0092-8674(00)80065-3 · Cited by 126
A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses
Sun, D., Lee, G., Lee, J. H., Kim, H. Y., Rhee, H., Park, S., Kim, K. J., Kim, Y., Kim, B. Y., Hong, J.-I., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1906 · Cited by 125
“A search for the structural homologs of MESH1 identified several His-Asp–box–containing metallophosphohydrolase”
BackgroundSchumacher, M. A., Scott, D. M., Mathews, I. I., Ealick, S. E., Roos, D. S., Ullman, B., & Brennan, R. G. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3753 · Cited by 125
Hidaka, M., Fushinobu, S., Ohtsu, N., Motoshima, H., Matsuzawa, H., Shoun, H., & Wakagi, T. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00746-5 · Cited by 128
Korndörfer, I. P., Danzer, J. F., Schmelcher, M., et al. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.08.069 · Cited by 125
Sierk, M. L., & Kleywegt, G. J. (2004) · Structure · doi:10.1016/j.str.2004.09.016 · Cited by 126
Structural basis of cell-cell adhesion by NCAM.
Larsen, I. K., Kasper, C., Rasmussen, H. B., et al. (2000) · Nature Structural Biology · doi:10.1038/75165 · Cited by 125
Pandini, A., Soshilov, A. A., Song, Y., Zhao, J., Bonati, L., & Denison, M. S. (2009) · Biochemistry · doi:10.1021/bi900259z · Cited by 124
“The templates were structurally aligned according to DALI-Lite (36,37).”
Insights into the Structure, Mechanism, and Regulation of Scavenger mRNA Decapping Activity
Gu, M., Fàbrega, C., Liu, S.-W., et al. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00180-7 · Cited by 124
Hagelueken, G., Adams, T., Wiehlmann, L., Widow, U., Kolmar, H., Tümmler, B., Heinz, D. W., & Schubert, W. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510501103 · Cited by 122
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
Roovers, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh191 · Cited by 124
“Analysis of the Protein Data Bank with the DALI program (48) revealed another protein with a quaternary structure very similar to the TrmI MTase (32).”
MethodCrystal Structure of Rat Bcl-xL
Aritomi, M., KUNISHIMA, N., Inohara, N., et al. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.44.27886 · Cited by 124
Mulepati, S., & Bailey, S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.270017 · Cited by 123
Crystal structure of TIPE2 provides insights into immune homeostasis
Zhang, X., Wang, J., Fan, C., et al. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1522 · Cited by 123
Dixon, M. M., Huang, S., Matthews, R. G., & Ludwig, M. L. (1996) · Structure · doi:10.1016/s0969-2126(96)00135-9 · Cited by 128
Kim, M. H., Choi, W., Kang, H. O., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504996102 · Cited by 123
A novel fucose recognition fold involved in innate immunity
Bianchet, M. A., Odom, E. W., Vasta, G. R., & Amzel, L. M. (2002) · Nature Structural Biology · doi:10.1038/nsb817 · Cited by 123
“However, a search for similar structures in the DALI databas”
BackgroundSolution Structure of the Cysteine-rich Domain of the Escherichia coli Chaperone Protein DnaJ
Martinez‐Yamout, M. A., Legge, G. B., Zhang, O., Wright, P. E., & Dyson, H. J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3923 · Cited by 122
García‐Mayoral, M. F., Hollingworth, D., Masino, L., Díaz‐Moreno, I., Kelly, G. P., Gherzi, R., Chou, C., Chen, C., & Ramos, A. (2007) · Structure · doi:10.1016/j.str.2007.03.006 · Cited by 123
“A structural alignment between KH3 (Gly 324-Arg 394) and KH4 (Gly 425-Gly 503) using the DALI (Holm and Sander, 1993) database server has returned a z score value of 9.”
MethodInfluentialPrates, J. A. M., Tarbouriech, N., Charnock, S. J., et al. (2001) · Structure · doi:10.1016/s0969-2126(01)00684-0 · Cited by 123
Hou, J., Jun, S., Zhang, C., & Kim, S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409772102 · Cited by 123
Metadata
- Authors
- Holm, L., & Sander, C.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1993-09
- Volume
- 233
- Issue
- 1
- Pages
- 123-138
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2022058405
- Cited by
- 3,984
- References
- 0
- Citations by year
- 2026: 23 · 2025: 31 · 2024: 22 · 2023: 22 · 2022: 28 · 2021: 27 · 2020: 53 · 2019: 50 · 2018: 45 · 2017: 42 · 2016: 53 · 2015: 65 · 2014: 73 · 2013: 106 · 2012: 98
- FWCI
- 15.32
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- protein structure comparison, Dali, Monte Carlo optimization, structural similarity, protein fold classification, structural core, colicin A, globin, lambda repressor, sequence gaps
- MeSH terms
- Actins, Algorithms, Amino Acid Sequence, Colicins, DNA-Binding Proteins, Globins, Heat-Shock Proteins, Hexokinase, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Muramidase, Software, Reproducibility of Results, Cluster Analysis, Sequence Alignment, Sequence Homology, Amino Acid, Protein Structure, Secondary, Protein Structure, Tertiary
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