PDBsum entry 1jl5

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Toxin PDB id
Protein chain
353 a.a. *
_CA ×5
Waters ×339
* Residue conservation analysis
PDB id:
Name: Toxin
Title: Novel molecular architecture of yopm-a leucine-rich effector protein from yersinia pestis
Structure: Outer protein yopm. Chain: a. Engineered: yes
Source: Yersinia pestis. Organism_taxid: 632. Gene: yopm. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
2.10Å     R-factor:   0.220     R-free:   0.240
Authors: A.G.Evdokimov,D.E.Anderson,K.M.Routzahn,D.S.Waugh
Key ref:
A.G.Evdokimov et al. (2001). Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit. J Mol Biol, 312, 807-821. PubMed id: 11575934 DOI: 10.1006/jmbi.2001.4973
15-Jul-01     Release date:   10-Oct-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P17778  (YOPM_YERPE) -  Outer membrane protein YopM
409 a.a.
353 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1006/jmbi.2001.4973 J Mol Biol 312:807-821 (2001)
PubMed id: 11575934  
Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit.
A.G.Evdokimov, D.E.Anderson, K.M.Routzahn, D.S.Waugh.
Many Gram-negative bacterial pathogens employ a contact-dependent (type III) secretion system to deliver effector proteins into the cytosol of animal or plant cells. Collectively, these effectors enable the bacteria to evade the immune response of the infected organism by modulating host-cell functions. YopM, a member of the leucine-rich repeat protein superfamily, is an effector produced by the bubonic plague bacterium, Yersinia pestis, that is essential for virulence. Here, we report crystal structures of YopM at 2.4 and 2.1 A resolution. Among all leucine-rich repeat family members whose atomic coordinates have been reported, the repeating unit of YopM has the least canonical secondary structure. In both crystals, four YopM monomers form a hollow cylinder with an inner diameter of 35 A. The domain that targets YopM for translocation into eukaryotic cells adopts a well-ordered, alpha-helical conformation that packs tightly against the proximal leucine-rich repeat module. A similar alpha-helical domain can be identified in virulence-associated leucine-rich repeat proteins produced by Salmonella typhimurium and Shigella flexneri, and in the conceptual translation products of several open reading frames in Y. pestis.
  Selected figure(s)  
Figure 6.
Figure 6. Least-squares superimposition of the 20-residue LRR from YopM (LRR13, red) with representative LRRs (green) from: (a) internalin B; (b) Rab geranylgeranyltransferase; (c) rna1p; (d) RNase inhibitor; and (e) U2A' spliceosomal protein.
Figure 11.
Figure 11. The Y. pestis YopM tetramer. (a) Two views of the YopM tetramer C^a-trace colored by monomer. (b) Molecular surface representation of the YopM tetramer and of the pairwise interactions of its constituent monomers. (c) Schematic representation of the calcium-binding sites.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 312, 807-821) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460456 E.Krissinel (2011).
Macromolecular complexes in crystals and solutions.
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Structural basis of steroid hormone perception by the receptor kinase BRI1.
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PDB codes: 3riz 3rj0
20877914 G.W.Buchko, G.Niemann, E.S.Baker, M.E.Belov, R.D.Smith, F.Heffron, J.N.Adkins, and J.E.McDermott (2010).
A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins.
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20515922 J.B.McPhee, P.Mena, and J.B.Bliska (2010).
Delineation of regions of the Yersinia YopM protein required for interaction with the RSK1 and PRK2 host kinases and their requirement for interleukin-10 production and virulence.
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Yersinia virulence factor YopM induces sustained RSK activation by interfering with dephosphorylation.
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20368345 M.W.McCoy, M.L.Marré, C.F.Lesser, and J.Mecsas (2010).
The C-terminal tail of Yersinia pseudotuberculosis YopM is critical for interacting with RSK1 and for virulence.
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20186337 V.Soundararajan, R.Raman, S.Raguram, V.Sasisekharan, and R.Sasisekharan (2010).
Atomic interaction networks in the core of protein domains and their native folds.
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A family of Salmonella virulence factors functions as a distinct class of autoregulated E3 ubiquitin ligases.
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PDB code: 3g06
19593816 E.Kloss, and D.Barrick (2009).
C-terminal deletion of leucine-rich repeats from YopM reveals a heterogeneous distribution of stability in a cooperatively folded protein.
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Quantitative analysis and prediction of curvature in leucine-rich repeat proteins.
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Structural and molecular mechanism for autoprocessing of MARTX toxin of Vibrio cholerae at multiple sites.
  J Biol Chem, 284, 26557-26568.
PDB code: 3fzy
19581396 Z.Ye, E.J.Kerschen, D.A.Cohen, A.M.Kaplan, N.van Rooijen, and S.C.Straley (2009).
Gr1+ cells control growth of YopM-negative yersinia pestis during systemic plague.
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18299249 F.Shao (2008).
Biochemical functions of Yersinia type III effectors.
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18081726 J.E.Trosky, A.D.Liverman, and K.Orth (2008).
Yersinia outer proteins: Yops.
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18343833 J.Huang, B.Hao, F.Deng, X.Sun, H.Wang, and Z.Hu (2008).
Open reading frame Bm21 of Bombyx mori nucleopolyhedrovirus is not essential for virus replication in vitro, but its deletion extends the median survival time of infected larvae.
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Comparative structural analysis of the binding domain of follicle stimulating hormone receptor.
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18423054 W.Viratyosin, S.Ingsriswang, E.Pacharawongsakda, and P.Palittapongarnpim (2008).
Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches.
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18997779 Y.Zhu, H.Li, L.Hu, J.Wang, Y.Zhou, Z.Pang, L.Liu, and F.Shao (2008).
Structure of a Shigella effector reveals a new class of ubiquitin ligases.
  Nat Struct Mol Biol, 15, 1302-1308.
PDB code: 3cvr
17517123 N.Matsushima, T.Tanaka, P.Enkhbayar, T.Mikami, M.Taga, K.Yamada, and Y.Kuroki (2007).
Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors.
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17603913 P.He, Y.Y.Sheng, Y.Z.Shi, X.G.Jiang, J.H.Qin, Z.M.Zhang, G.P.Zhao, and X.K.Guo (2007).
Genetic diversity among major endemic strains of Leptospira interrogans in China.
  BMC Genomics, 8, 204.  
17057330 A.Ooi, S.Hussain, A.Seyedarabi, and R.W.Pickersgill (2006).
Structure of internalin C from Listeria monocytogenes.
  Acta Crystallogr D Biol Crystallogr, 62, 1287-1293.
PDB code: 1xeu
16385027 J.Waldemarsson, T.Areschoug, G.Lindahl, and E.Johnsson (2006).
The streptococcal Blr and Slr proteins define a family of surface proteins with leucine-rich repeats: camouflaging by other surface structures.
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16990280 Y.Mochida, D.Parisuthiman, M.Kaku, J.Hanai, V.P.Sukhatme, and M.Yamauchi (2006).
Nephrocan, a novel member of the small leucine-rich repeat protein family, is an inhibitor of transforming growth factor-beta signaling.
  J Biol Chem, 281, 36044-36051.  
15847602 G.I.Viboud, and J.B.Bliska (2005).
Yersinia outer proteins: role in modulation of host cell signaling responses and pathogenesis.
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16098210 J.A.Sorg, N.C.Miller, and O.Schneewind (2005).
Substrate recognition of type III secretion machines--testing the RNA signal hypothesis.
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15961631 J.Choe, M.S.Kelker, and I.A.Wilson (2005).
Crystal structure of human toll-like receptor 3 (TLR3) ectodomain.
  Science, 309, 581-585.
PDB code: 1ziw
16043704 J.K.Bell, I.Botos, P.R.Hall, J.Askins, J.Shiloach, D.M.Segal, and D.R.Davies (2005).
The molecular structure of the Toll-like receptor 3 ligand-binding domain.
  Proc Natl Acad Sci U S A, 102, 10976-10980.
PDB code: 2a0z
16164979 K.A.Dickson, M.C.Haigis, and R.T.Raines (2005).
Ribonuclease inhibitor: structure and function.
  Prog Nucleic Acid Res Mol Biol, 80, 349-374.  
15271922 A.Ikegami, K.Honma, A.Sharma, and H.K.Kuramitsu (2004).
Multiple functions of the leucine-rich repeat protein LrrA of Treponema denticola.
  Infect Immun, 72, 4619-4627.  
15272862 A.P.Tampakaki, V.E.Fadouloglou, A.D.Gazi, N.J.Panopoulos, and M.Kokkinidis (2004).
Conserved features of type III secretion.
  Cell Microbiol, 6, 805-816.  
15093830 H.Remaut, and G.Waksman (2004).
Structural biology of bacterial pathogenesis.
  Curr Opin Struct Biol, 14, 161-170.  
14734555 L.B.Clark, P.Viswanathan, G.Quigley, Y.C.Chiang, J.S.McMahon, G.Yao, J.Chen, A.Nelsbach, and C.L.Denis (2004).
Systematic mutagenesis of the leucine-rich repeat (LRR) domain of CCR4 reveals specific sites for binding to CAF1 and a separate critical role for the LRR in CCR4 deadenylase activity.
  J Biol Chem, 279, 13616-13623.  
14747988 P.Enkhbayar, M.Kamiya, M.Osaki, T.Matsumoto, and N.Matsushima (2004).
Structural principles of leucine-rich repeat (LRR) proteins.
  Proteins, 54, 394-403.  
15590783 P.Ghosh (2004).
Process of protein transport by the type III secretion system.
  Microbiol Mol Biol Rev, 68, 771-795.  
15048835 R.Das, and M.Gerstein (2004).
A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens.
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15009029 R.Hoffmann, K.van Erp, K.Trülzsch, and J.Heesemann (2004).
Transcriptional responses of murine macrophages to infection with Yersinia enterocolitica.
  Cell Microbiol, 6, 377-390.  
15225308 S.Cunnac, A.Occhialini, P.Barberis, C.Boucher, and S.Genin (2004).
Inventory and functional analysis of the large Hrp regulon in Ralstonia solanacearum: identification of novel effector proteins translocated to plant host cells through the type III secretion system.
  Mol Microbiol, 53, 115-128.  
12631703 A.Blocker, K.Komoriya, and S.Aizawa (2003).
Type III secretion systems and bacterial flagella: insights into their function from structural similarities.
  Proc Natl Acad Sci U S A, 100, 3027-3030.  
12904578 A.Di Matteo, L.Federici, B.Mattei, G.Salvi, K.A.Johnson, C.Savino, G.De Lorenzo, D.Tsernoglou, and F.Cervone (2003).
The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense.
  Proc Natl Acad Sci U S A, 100, 10124-10128.
PDB code: 1ogq
14506477 C.E.Stebbins, and J.E.Galán (2003).
Priming virulence factors for delivery into the host.
  Nat Rev Mol Cell Biol, 4, 738-743.  
12626518 C.McDonald, P.O.Vacratsis, J.B.Bliska, and J.E.Dixon (2003).
The yersinia virulence factor YopM forms a novel protein complex with two cellular kinases.
  J Biol Chem, 278, 18514-18523.  
12540576 E.Skrzypek, T.Myers-Morales, S.W.Whiteheart, and S.C.Straley (2003).
Application of a Saccharomyces cerevisiae model to study requirements for trafficking of Yersinia pestis YopM in eucaryotic cells.
  Infect Immun, 71, 937-947.  
12601001 P.G.Scott, J.G.Grossmann, C.M.Dodd, J.K.Sheehan, and P.N.Bishop (2003).
Light and X-ray scattering show decorin to be a dimer in solution.
  J Biol Chem, 278, 18353-18359.  
14638794 S.D.Reid, A.G.Montgomery, J.M.Voyich, F.R.DeLeo, B.Lei, R.M.Ireland, N.M.Green, M.Liu, S.Lukomski, and J.M.Musser (2003).
Characterization of an extracellular virulence factor made by group A Streptococcus with homology to the Listeria monocytogenes internalin family of proteins.
  Infect Immun, 71, 7043-7052.  
12839991 W.A.Barton, B.P.Liu, D.Tzvetkova, P.D.Jeffrey, A.E.Fournier, D.Sah, R.Cate, S.M.Strittmatter, and D.B.Nikolov (2003).
Structure and axon outgrowth inhibitor binding of the Nogo-66 receptor and related proteins.
  EMBO J, 22, 3291-3302.
PDB code: 1p8t
14661268 W.D.Schubert, and D.W.Heinz (2003).
Structural aspects of adhesion to and invasion of host cells by the human pathogen Listeria monocytogenes.
  Chembiochem, 4, 1285-1291.  
12360191 G.R.Cornelis (2002).
The Yersinia Ysc-Yop 'type III' weaponry.
  Nat Rev Mol Cell Biol, 3, 742-752.  
12163464 G.R.Cornelis (2002).
Yersinia type III secretion: send in the effectors.
  J Cell Biol, 158, 401-408.  
12226088 H.Ceulemans, V.Vulsteke, M.De Maeyer, K.Tatchell, W.Stalmans, and M.Bollen (2002).
Binding of the concave surface of the Sds22 superhelix to the alpha 4/alpha 5/alpha 6-triangle of protein phosphatase-1.
  J Biol Chem, 277, 47331-47337.  
12526809 W.D.Schubert, C.Urbanke, T.Ziehm, V.Beier, M.P.Machner, E.Domann, J.Wehland, T.Chakraborty, and D.W.Heinz (2002).
Structure of internalin, a major invasion protein of Listeria monocytogenes, in complex with its human receptor E-cadherin.
  Cell, 111, 825-836.
PDB codes: 1o6s 1o6t 1o6v
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.