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PDBsum entry 1ukf

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protein links
Hydrolase PDB id
1ukf
Jmol
Contents
Protein chain
188 a.a. *
Waters ×197
* Residue conservation analysis
PDB id:
1ukf
Name: Hydrolase
Title: Crystal structure of pseudomonas avirulence protein avrpphb
Structure: Avirulence protein avrpph3. Chain: a. Fragment: residues 81-267. Synonym: pseudomonas avrpphb. Engineered: yes
Source: Pseudomonas syringae pv. Phaseolicola. Organism_taxid: 319. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.35Å     R-factor:   0.204     R-free:   0.222
Authors: M.Zhu,F.Shao,R.W.Innes,J.E.Dixon,Z.Xu
Key ref:
M.Zhu et al. (2004). The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site. Proc Natl Acad Sci U S A, 101, 302-307. PubMed id: 14694194 DOI: 10.1073/pnas.2036536100
Date:
21-Aug-03     Release date:   09-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q52430  (AVRP3_PSESH) -  Cysteine protease avirulence protein AvrPphB
Seq:
Struc:
267 a.a.
188 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     pathogenesis   1 term 
  Biochemical function     cysteine-type endopeptidase activity     1 term  

 

 
DOI no: 10.1073/pnas.2036536100 Proc Natl Acad Sci U S A 101:302-307 (2004)
PubMed id: 14694194  
 
 
The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site.
M.Zhu, F.Shao, R.W.Innes, J.E.Dixon, Z.Xu.
 
  ABSTRACT  
 
AvrPphB is an avirulence (Avr) protein from the plant pathogen Pseudomonas syringae that can trigger a disease-resistance response in a number of host plants including Arabidopsis. AvrPphB belongs to a novel family of cysteine proteases with the charter member of this family being the Yersinia effector protein YopT. AvrPphB has a very stringent substrate specificity, catalyzing a single proteolytic cleavage in the Arabidopsis serine/threonine kinase PBS1. We have determined the crystal structure of AvrPphB by x-ray crystallography at 1.35-A resolution. The structure is composed of a central antiparallel beta-sheet, with alpha-helices packing on both sides of the sheet to form a two-lobe structure. The core of this structure resembles the papain-like cysteine proteases. The similarity includes the AvrPphB active site catalytic triad of Cys-98, His-212, and Asp-227 and the oxyanion hole residue Asn-93. Based on analogy with inhibitor complexes of the papain-like proteases, we propose a model for the substrate-binding mechanism of AvrPphB. A deep and positively charged pocket (S2) and a neighboring shallow surface (S3) likely bind to aspartic acid and glycine residues in the substrate located two (P2) and three (P3) residues N terminal to the cleavage site, respectively. Further implications about the specificity of plant pathogen recognition are also discussed.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Electron density map of AvrPphB. Stereo pair of a [A]-weighed 2|F[o]| - |F[c]| simulated-annealing omit electron density map (1.35 Å, contoured at 1.2 ) calculated with the final refined coordinates. Shown here is a region near the catalytic triad. The region includes highly conserved residues Trp-105, Asp-227 (one of the catalytic triad residues), Pro-228, Asn-229, Gly-231, Glu-232, and Phe-233. Notably, the rings of Trp-105, Phe-226, and Pro-228 are stacked on each other. The image was prepared with the program MOLSCRIPT.
Figure 5.
Fig. 5. The structural basis of AvrPphB substrate specificity. (A) Sequence comparison of AvrPphB cleavage sites in its precursor and substrate PBS1 protein. A common Gly-Asp-Lys motif preceding the cleavage sites is highlighted in red, and the arrow indicates the cleavage sites. (B and C) Active site clefts of papain-like enzyme and AvrPphB. Orientation is the same as in Fig. 4A. B shows the molecular surface of cruzain (PDB ID code 2aim [PDB] ), and C shows that of AvrPphB. The structure of cruzain was determined with the inhibitor benzoyl-Arg-Ala-fluoromethyl ketone, which occupies the S3, S2, and S1 sites and is shown in B Left as a CPK representation. C Right is a zoom-in view of the proposed active site of AvrPphB. The proposed S2 site residue (Arg-205) and four catalytically important residues are drawn underneath the molecular surface. Note the positive character of S2 and shallowness of S3 at the substrate-binding site. All surfaces are colored based on the electrostatic potential of the molecule (ranging from -23 to +23 kT). Images were prepared with the program GRASP (53).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151626 S.S.Bhaskaran, and C.E.Stebbins (2012).
Structure of the catalytic domain of the Salmonella virulence factor SseI.
  Acta Crystallogr D Biol Crystallogr, 68, 1613-1621.
PDB codes: 4g29 4g2b
22407319 T.Sanada, M.Kim, H.Mimuro, M.Suzuki, M.Ogawa, A.Oyama, H.Ashida, T.Kobayashi, T.Koyama, S.Nagai, Y.Shibata, J.Gohda, J.Inoue, T.Mizushima, and C.Sasakawa (2012).
The Shigella flexneri effector OspI deamidates UBC13 to dampen the inflammatory response.
  Nature, 483, 623-626.
PDB code: 3b21
19440549 A.Crow, P.R.Race, G.Jubelin, C.Varela Chavez, J.M.Escoubas, E.Oswald, and M.J.Banfield (2009).
Crystal Structures of Cif from Bacterial Pathogens Photorhabdus luminescens and Burkholderia pseudomallei.
  PLoS ONE, 4, e5582.
PDB codes: 3gqj 3gqm
19540926 J.D.Lewis, D.S.Guttman, and D.Desveaux (2009).
The targeting of plant cellular systems by injected type III effector proteins.
  Semin Cell Dev Biol, 20, 1055-1063.  
19849780 J.W.Mansfield (2009).
From bacterial avirulence genes to effector functions via the hrp delivery system: an overview of 25 years of progress in our understanding of plant innate immunity.
  Mol Plant Pathol, 10, 721-734.  
19019163 K.Kambara, S.Ardissone, H.Kobayashi, M.M.Saad, O.Schumpp, W.J.Broughton, and W.J.Deakin (2009).
Rhizobia utilize pathogen-like effector proteins during symbiosis.
  Mol Microbiol, 71, 92.  
19849784 K.R.Munkvold, and G.B.Martin (2009).
Advances in experimental methods for the elucidation of Pseudomonas syringae effector function with a focus on AvrPtoB.
  Mol Plant Pathol, 10, 777-793.  
19225106 Q.Yao, J.Cui, Y.Zhu, G.Wang, L.Hu, C.Long, R.Cao, X.Liu, N.Huang, S.Chen, L.Liu, and F.Shao (2009).
A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle.
  Proc Natl Acad Sci U S A, 106, 3716-3721.
PDB codes: 3eir 3eit
19346252 R.H.Dowen, J.L.Engel, F.Shao, J.R.Ecker, and J.E.Dixon (2009).
A family of bacterial cysteine protease type III effectors utilizes acylation-dependent and -independent strategies to localize to plasma membranes.
  J Biol Chem, 284, 15867-15879.  
18299249 F.Shao (2008).
Biochemical functions of Yersinia type III effectors.
  Curr Opin Microbiol, 11, 21-29.  
17993455 N.Mallorquí-Fernández, S.P.Manandhar, G.Mallorquí-Fernández, I.Usón, K.Wawrzonek, T.Kantyka, M.Solà, I.B.Thøgersen, J.J.Enghild, J.Potempa, and F.X.Gomis-Rüth (2008).
A new autocatalytic activation mechanism for cysteine proteases revealed by Prevotella intermedia interpain A.
  J Biol Chem, 283, 2871-2882.
PDB codes: 3bb7 3bba
18418689 O.Riess, U.Rüb, A.Pastore, P.Bauer, and L.Schöls (2008).
SCA3: Neurological features, pathogenesis and animal models.
  Cerebellum, 7, 125-137.  
18487326 W.J.Dai, Y.Zeng, Z.P.Xie, and C.Staehelin (2008).
Symbiosis-promoting and deleterious effects of NopT, a novel type 3 effector of Rhizobium sp. strain NGR234.
  J Bacteriol, 190, 5101-5110.  
18845161 Y.Hsu, G.Jubelin, F.Taieb, J.P.Nougayrède, E.Oswald, and C.E.Stebbins (2008).
Structure of the cyclomodulin Cif from pathogenic Escherichia coli.
  J Mol Biol, 384, 465-477.
PDB code: 3efy
17360394 K.Kitadokoro, S.Kamitani, M.Miyazawa, M.Hanajima-Ozawa, A.Fukui, M.Miyake, and Y.Horiguchi (2007).
Crystal structures reveal a thiol protease-like catalytic triad in the C-terminal region of Pasteurella multocida toxin.
  Proc Natl Acad Sci U S A, 104, 5139-5144.
PDB codes: 2ebf 2ebh 2ec5
17179076 L.E.Rose, R.W.Michelmore, and C.H.Langley (2007).
Natural variation in the Pto disease resistance gene within species of wild tomato (Lycopersicon). II. Population genetics of Pto.
  Genetics, 175, 1307-1319.  
16713730 D.Desveaux, A.U.Singer, and J.L.Dangl (2006).
Type III effector proteins: doppelgangers of bacterial virulence.
  Curr Opin Plant Biol, 9, 376-382.  
16792692 M.de Torres, J.W.Mansfield, N.Grabov, I.R.Brown, H.Ammouneh, G.Tsiamis, A.Forsyth, S.Robatzek, M.Grant, and J.Boch (2006).
Pseudomonas syringae effector AvrPtoB suppresses basal defence in Arabidopsis.
  Plant J, 47, 368-382.  
16753033 S.R.Grant, E.J.Fisher, J.H.Chang, B.M.Mole, and J.L.Dangl (2006).
Subterfuge and manipulation: type III effector proteins of phytopathogenic bacteria.
  Annu Rev Microbiol, 60, 425-449.  
16913834 T.Sulea, H.A.Lindner, and R.Ménard (2006).
Structural aspects of recently discovered viral deubiquitinating activities.
  Biol Chem, 387, 853-862.  
16978145 V.V.Mosolov, and T.A.Valueva (2006).
Participation of proteolytic enzymes in the interaction of plants with phytopathogenic microorganisms.
  Biochemistry (Mosc), 71, 838-845.  
16046625 C.R.Büttner, G.R.Cornelis, D.W.Heinz, and H.H.Niemann (2005).
Crystal structure of Yersinia enterocolitica type III secretion chaperone SycT.
  Protein Sci, 14, 1993-2002.
PDB codes: 2bsh 2bsi 2bsj
15847602 G.I.Viboud, and J.B.Bliska (2005).
Yersinia outer proteins: role in modulation of host cell signaling responses and pathogenesis.
  Annu Rev Microbiol, 59, 69-89.  
16020535 G.Nicastro, R.P.Menon, L.Masino, P.P.Knowles, N.Q.McDonald, and A.Pastore (2005).
The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition.
  Proc Natl Acad Sci U S A, 102, 10493-10498.
PDB code: 1yzb
15964983 J.H.Lee, J.M.Choi, C.Lee, K.J.Yi, and Y.Cho (2005).
Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.
  Proc Natl Acad Sci U S A, 102, 9144-9149.
PDB codes: 1x3w 1x3z
15862106 M.B.Mudgett (2005).
New insights to the function of phytopathogenic bacterial type III effectors in plants.
  Annu Rev Plant Biol, 56, 509-531.  
15231260 A.Hotson, and M.B.Mudgett (2004).
Cysteine proteases in phytopathogenic bacteria: identification of plant targets and activation of innate immunity.
  Curr Opin Plant Biol, 7, 384-390.  
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.  
15283671 J.R.Alfano, and A.Collmer (2004).
Type III secretion system effector proteins: double agents in bacterial disease and plant defense.
  Annu Rev Phytopathol, 42, 385-414.  
15574492 K.Wenig, L.Chatwell, U.von Pawel-Rammingen, L.Björck, R.Huber, and P.Sondermann (2004).
Structure of the streptococcal endopeptidase IdeS, a cysteine proteinase with strict specificity for IgG.
  Proc Natl Acad Sci U S A, 101, 17371-17376.
PDB code: 1y08
15447649 P.Coppinger, P.P.Repetti, B.Day, D.Dahlbeck, A.Mehlert, and B.J.Staskawicz (2004).
Overexpression of the plasma membrane-localized NDR1 protein results in enhanced bacterial disease resistance in Arabidopsis thaliana.
  Plant J, 40, 225-237.  
15339266 Y.Xia (2004).
Proteases in pathogenesis and plant defence.
  Cell Microbiol, 6, 905-913.  
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.