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PDBsum entry 1vr0

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1vr0
Jmol
Contents
Protein chains
236 a.a. *
Ligands
3SL ×3
Metals
_MG ×2
Waters ×93
* Residue conservation analysis
PDB id:
1vr0
Name: Hydrolase
Title: Crystal structure of putative 2-phosphosulfolactate phosphat (15026306) from clostridium acetobutylicum at 2.6 a resolut
Structure: Probable 2-phosphosulfolactate phosphatase. Chain: a, b, c. Engineered: yes
Source: Clostridium acetobutylicum. Organism_taxid: 1488. Gene: comb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.49Å     R-factor:   0.192     R-free:   0.229
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
M.DiDonato et al. (2006). Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site. Proteins, 65, 771-776. PubMed id: 16927339 DOI: 10.1002/prot.20978
Date:
26-Jan-05     Release date:   15-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q97E82  (COMB_CLOAB) -  Probable 2-phosphosulfolactate phosphatase
Seq:
Struc:
235 a.a.
236 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.71  - 2-phosphosulfolactate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Coenzyme M Biosynthesis
      Reaction: (2R)-2-phospho-3-sulfolactate + H2O = (2R)-3-sulfolactate + phosphate
(2R)-2-phospho-3-sulfolactate
+ H(2)O
=
(2R)-3-sulfolactate
Bound ligand (Het Group name = 3SL)
corresponds exactly
+ phosphate
      Cofactor: Magnesium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     dephosphorylation   2 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.20978 Proteins 65:771-776 (2006)
PubMed id: 16927339  
 
 
Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site.
M.DiDonato, S.S.Krishna, R.Schwarzenbacher, D.McMullan, S.Agarwalla, S.M.Brittain, M.D.Miller, P.Abdubek, E.Ambing, H.L.Axelrod, J.M.Canaves, H.J.Chiu, A.M.Deacon, L.Duan, M.A.Elsliger, A.Godzik, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, K.Quijano, R.Reyes, C.L.Rife, G.Spraggon, R.C.Stevens, H.van den Bedem, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure and reaction of ComB. A: Scheme for the reaction performed by ComB (EC 3.1.3.71), which catalyzes the hydrolysis of (2R)-2-phospho-3-sulfolactate yielding (2R)-3-sulfolactate and phosphate. B: Crystal structure of ComB. Ribbon diagram showing the domain organization with N-terminal domain (cyan), middle domain (yellow), and C-terminal region (purple). Helices H1-H13, -strands ( 1- 10), the magnesium ion (purple sphere), and (2R)-3-sulfolactate (ball-and-stick) are indicated. C: Diagram showing the secondary structural elements in ComB superimposed on its primary sequence. The -helices, -strands (indicated by red A), -bulges, and -turns are indicated. The -hairpin is depicted as a red loop. Residues coordinating the magnesium ion and ligand molecule are marked with blue and red circles, respectively.
Figure 2.
Figure 2. Structural comparison and active site of ComB. A: First domain of ComB (PDB 1vr0, chain A: 1-27, 104-177). B: The structural core of PTPase II (PDB 1vhr, chain A: 35-143) C: Structural core of PTPase I (PDB 1phr, chain A: 4-157). In panels A-C, the -strands are labeled. The -helices are colored cyan, -strands are colored in yellow. Regions corresponding to the general location of the active site in these structures are colored red. D: Structure-based sequence alignment of the first (1vr0_1) and second (1vr0_2) domains of ComB. A consensus pattern of hydrophobic and polar residues is shown. Identical residues are shown in bold. Polar amino acids are highlighted in gray and hydrophobic residues in yellow. The start and end residues of the domains are shown. Regions corresponding to long insertions were omitted for clarity, and the number of omitted residues is specified in brackets. Regions of circular permutation are separated by a | mark, and the sequence number of the residues around the permuted region are shown in red. E: Stereo diagram of ComB active site. The bound product 3SL [(2R)-3-sulfolactate] and active site residues of ComB are depicted in ball-and-stick, with the magnesium ion shown as a purple sphere. F: ComB dimer (green, gray) in ribbon representation, with the 3SL [(2R)-3-sulfolactate] molecule (carbon, yellow; oxygen, red; and phosphorus, orange) and magnesium ion (purple/gray) depicted in spheres.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 771-776) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19465773 T.C.Terwilliger, P.D.Adams, R.J.Read, A.J.McCoy, N.W.Moriarty, R.W.Grosse-Kunstleve, P.V.Afonine, P.H.Zwart, and L.W.Hung (2009).
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
  Acta Crystallogr D Biol Crystallogr, 65, 582-601.  
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