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PDBsum entry 1n57

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protein metals links
Chaperone PDB id
1n57
Jmol
Contents
Protein chain
279 a.a. *
Metals
_MG
Waters ×353
* Residue conservation analysis
PDB id:
1n57
Name: Chaperone
Title: Crystal structure of chaperone hsp31
Structure: Chaperone hsp31. Chain: a. Synonym: protein yedu. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: hcha/yedu. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.60Å     R-factor:   0.190     R-free:   0.242
Authors: P.M.Quigley,K.Korotkov,F.Baneyx,W.G.J.Hol
Key ref:
P.M.Quigley et al. (2003). The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad. Proc Natl Acad Sci U S A, 100, 3137-3142. PubMed id: 12621151 DOI: 10.1073/pnas.0530312100
Date:
04-Nov-02     Release date:   18-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P31658  (HCHA_ECOLI) -  Molecular chaperone Hsp31 and glyoxalase 3
Seq:
Struc:
283 a.a.
279 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.130  - D-lactate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-lactate = methylglyoxal + H2O
(R)-lactate
= methylglyoxal
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     response to stress   6 terms 
  Biochemical function     protein binding     7 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0530312100 Proc Natl Acad Sci U S A 100:3137-3142 (2003)
PubMed id: 12621151  
 
 
The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad.
P.M.Quigley, K.Korotkov, F.Baneyx, W.G.Hol.
 
  ABSTRACT  
 
Heat shock proteins (Hsps) play essential protective roles under stress conditions by preventing the formation of protein aggregates and degrading misfolded proteins. EcHsp31, the yedU (hchA) gene product, is a representative member of a family of chaperones that alleviates protein misfolding by interacting with early unfolding intermediates. The 1.6-A crystal structure of the EcHsp31 dimer reveals a system of hydrophobic patches, canyons, and grooves, which may stabilize partially unfolded substrate. The presence of a well conserved, yet buried, triad in each two-domain subunit suggests a still unproven hydrolytic function of the protein. A flexible extended linker between the A and P domains may play a role in conformational flexibility and substrate binding. The alpha-beta sandwich of the EcHsp31 monomer shows structural similarity to PhPI, a protease belonging to the DJ-1 superfamily. The structure-guided sequence alignment indicates that Hsp31 homologs can be divided in three classes based on variations in the P domain that dramatically affect both oligomerization and catalytic triad formation.
 
  Selected figure(s)  
 
Figure 1.
Fig 1. Ribbon representation of the EcHsp31 monomer. The A domain is blue, the P domain is green (P1-P3 segments are in progressively lighter shades of green), and the linker region is purple. The catalytic triad is shown as a red ball-and-stick model (28).
Figure 3.
Fig 3. Two views of ribbon representation of the EcHsp31 dimer. The A and P domains of subunit I are blue and green, respectively, and are pale blue and pale green for subunit II, respectively. The linker is purple and light purple for subunits I and II, respectively. The catalytic triads of both subunits are shown in the red ball-and-stick illustration (28). (A) View down the crystallographic twofold axis. (B) View perpendicular to the crystallographic twofold axis.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322020 F.Ghazavi, Z.Fazlali, S.S.Banihosseini, S.R.Hosseini, M.H.Kazemi, S.Shojaee, K.Parsa, H.Sadeghi, F.Sina, M.Rohani, G.A.Shahidi, N.Ghaemi, M.Ronaghi, and E.Elahi (2011).
PRKN, DJ-1, and PINK1 screening identifies novel splice site mutation in PRKN and two novel DJ-1 mutations.
  Mov Disord, 26, 80-89.  
20124404 F.Kthiri, H.T.Le, V.Gautier, T.Caldas, A.Malki, A.Landoulsi, C.Bohn, P.Bouloc, and G.Richarme (2010).
Protein aggregation in a mutant deficient in yajL, the bacterial homolog of the Parkinsonism-associated protein DJ-1.
  J Biol Chem, 285, 10328-10336.  
19517531 M.S.Sastry, W.Zhou, and F.Baneyx (2009).
Integrity of N- and C-termini is important for E. coli Hsp31 chaperone activity.
  Protein Sci, 18, 1439-1447.  
19686841 P.J.Kahle, J.Waak, and T.Gasser (2009).
DJ-1 and prevention of oxidative stress in Parkinson's disease and other age-related disorders.
  Free Radic Biol Med, 47, 1354-1361.  
18570440 A.C.Witt, M.Lakshminarasimhan, B.C.Remington, S.Hasim, E.Pozharski, and M.A.Wilson (2008).
Cysteine pKa depression by a protonated glutamic acid in human DJ-1.
  Biochemistry, 47, 7430-7440.
PDB codes: 2or3 3cy6 3cyf 3cz9 3cza
17847089 K.Goyal, and S.C.Mande (2008).
Exploiting 3D structural templates for detection of metal-binding sites in protein structures.
  Proteins, 70, 1206-1218.  
17933887 J.Abdallah, T.Caldas, F.Kthiri, R.Kern, and G.Richarme (2007).
YhbO protects cells against multiple stresses.
  J Bacteriol, 189, 9140-9144.  
17158627 M.Mujacic, and F.Baneyx (2007).
Chaperone Hsp31 contributes to acid resistance in stationary-phase Escherichia coli.
  Appl Environ Microbiol, 73, 1014-1018.  
  17277453 W.Liu, Y.Y.Zhou, M.K.Teng, and C.Z.Zhou (2007).
Purification, crystallization and preliminary X-ray analysis of Hsp33 from Saccharomyces cerevisiae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 114-116.  
17257049 Y.Wei, D.Ringe, M.A.Wilson, and M.J.Ondrechen (2007).
Identification of functional subclasses in the DJ-1 superfamily proteins.
  PLoS Comput Biol, 3, e10.  
16322566 M.B.Cannon, and S.J.Remington (2006).
Re-engineering redox-sensitive green fluorescent protein for improved response rate.
  Protein Sci, 15, 45-57.
PDB codes: 2ah8 2aha
16796689 M.Mujacic, and F.Baneyx (2006).
Regulation of Escherichia coli hchA, a stress-inducible gene encoding molecular chaperone Hsp31.
  Mol Microbiol, 60, 1576-1589.  
16438678 R.E.De Castro, J.A.Maupin-Furlow, M.I.Giménez, M.K.Herrera Seitz, and J.J.Sánchez (2006).
Haloarchaeal proteases and proteolytic systems.
  FEMS Microbiol Rev, 30, 17-35.  
15906321 A.J.Bordner, and R.Abagyan (2005).
Statistical analysis and prediction of protein-protein interfaces.
  Proteins, 60, 353-366.  
16022590 D.J.Moore, A.B.West, V.L.Dawson, and T.M.Dawson (2005).
Molecular pathophysiology of Parkinson's disease.
  Annu Rev Neurosci, 28, 57-87.  
15935068 M.C.Meulener, C.L.Graves, D.M.Sampathu, C.E.Armstrong-Gold, N.M.Bonini, and B.I.Giasson (2005).
DJ-1 is present in a large molecular complex in human brain tissue and interacts with alpha-synuclein.
  J Neurochem, 93, 1524-1532.  
15766664 R.H.Kim, M.Peters, Y.Jang, W.Shi, M.Pintilie, G.C.Fletcher, C.DeLuca, J.Liepa, L.Zhou, B.Snow, R.C.Binari, A.S.Manoukian, M.R.Bray, F.F.Liu, M.S.Tsao, and T.W.Mak (2005).
DJ-1, a novel regulator of the tumor suppressor PTEN.
  Cancer Cell, 7, 263-273.  
15112332 A.B.Siva, V.R.Sundareswaran, C.H.Yeung, T.G.Cooper, and S.Shivaji (2004).
Hamster contraception associated protein 1 (CAP1).
  Mol Reprod Dev, 68, 373-383.  
15516999 D.J.Selkoe (2004).
Cell biology of protein misfolding: the examples of Alzheimer's and Parkinson's diseases.
  Nat Cell Biol, 6, 1054-1061.  
15175075 E.I.Agorogiannis, G.I.Agorogiannis, A.Papadimitriou, and G.M.Hadjigeorgiou (2004).
Protein misfolding in neurodegenerative diseases.
  Neuropathol Appl Neurobiol, 30, 215-224.  
15144563 F.Baneyx (2004).
Keeping up with protein folding.
  Microb Cell Fact, 3, 6.  
15529165 F.Baneyx, and M.Mujacic (2004).
Recombinant protein folding and misfolding in Escherichia coli.
  Nat Biotechnol, 22, 1399-1408.  
15228534 H.Yamazaki, A.Tomono, Y.Ohnishi, and S.Horinouchi (2004).
DNA-binding specificity of AdpA, a transcriptional activator in the A-factor regulatory cascade in Streptomyces griseus.
  Mol Microbiol, 53, 555-572.  
14745011 M.A.Wilson, C.V.St Amour, J.L.Collins, D.Ringe, and G.A.Petsko (2004).
The 1.8-A resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: a member of the DJ-1/ThiJ/PfpI superfamily.
  Proc Natl Acad Sci U S A, 101, 1531-1536.
PDB codes: 1rw7 4qyx
15130476 M.Graille, S.Quevillon-Cheruel, N.Leulliot, C.Z.Zhou, I.Li de la Sierra Gallay, L.Jacquamet, J.L.Ferrer, D.Liger, A.Poupon, J.Janin, and H.van Tilbeurgh (2004).
Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family.
  Structure, 12, 839-847.
PDB codes: 1qvv 1qvw 1qvz
14731284 M.Mujacic, M.W.Bader, and F.Baneyx (2004).
Escherichia coli Hsp31 functions as a holding chaperone that cooperates with the DnaK-DnaJ-GrpE system in the management of protein misfolding under severe stress conditions.
  Mol Microbiol, 51, 849-859.  
15173574 M.S.Sastry, P.M.Quigley, W.G.Hol, and F.Baneyx (2004).
The linker-loop region of Escherichia coli chaperone Hsp31 functions as a gate that modulates high-affinity substrate binding at elevated temperatures.
  Proc Natl Acad Sci U S A, 101, 8587-8592.  
15272270 M.Vila, and S.Przedborski (2004).
Genetic clues to the pathogenesis of Parkinson's disease.
  Nat Med, 10, S58-S62.  
14691241 P.M.Quigley, K.Korotkov, F.Baneyx, and W.G.Hol (2004).
A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function.
  Protein Sci, 13, 269-277.
PDB code: 1pv2
15070401 S.Bandyopadhyay, and M.R.Cookson (2004).
Evolutionary and functional relationships within the DJ1 superfamily.
  BMC Evol Biol, 4, 6.  
12855764 M.A.Wilson, J.L.Collins, Y.Hod, D.Ringe, and G.A.Petsko (2003).
The 1.1-A resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease.
  Proc Natl Acad Sci U S A, 100, 9256-9261.
PDB code: 1p5f
14500888 Y.Zhao, D.Liu, W.D.Kaluarachchi, H.D.Bellamy, M.A.White, and R.O.Fox (2003).
The crystal structure of Escherichia coli heat shock protein YedU reveals three potential catalytic active sites.
  Protein Sci, 12, 2303-2311.
PDB code: 1ons
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.