PDBsum entry: 1vr0

Hydrolase

PDB id: 1vr0

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

Protein chains

Q97E82  (COMB_CLOAB) -  Probable 2-phosphosulfolactate phosphatase

Seq: 235 a.a.

Struc: 236 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.71 - 2-phosphosulfolactate phosphatase.
• 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 

• Biological process: coenzyme M biosynthetic process (1 term)
• 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.