PDBsum entry 1so5

Lyase

PDB id: 1so5

Contents

Protein chains

213 a.a. *

Ligands

TX4 ×2

Metals

_MG ×2

Waters ×383

* Residue conservation analysis

PDB id:

1so5

Name:

Lyase

Title:

Crystal structure of e112q mutant of 3-keto-l-gulonate 6-phosphate decarboxylase with bound l-threonohydroxamate 4-phosphate

Structure:

3-keto-l-gulonate 6-phosphate decarboxylase. Chain: a, b. Synonym: hexulose-6-phosphate synthase. Humps. D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ulad. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.158 R-free: 0.196

Authors:

E.L.Wise,W.S.Yew,J.A.Gerlt,I.Rayment

Key ref:

E.L.Wise et al. (2004). Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry, 43, 6438-6446. PubMed id: 15157078 DOI: 10.1021/bi0497392

Date:

12-Mar-04 Release date: 08-Jun-04

Protein chains

P39304  (ULAD_ECOLI) -  3-keto-L-gulonate-6-phosphate decarboxylase UlaD from Escherichia coli (strain K12)

Seq: 216 a.a.

Struc: 213 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.1.1.85 - 3-dehydro-L-gulonate-6-phosphate decarboxylase.
• Reaction: 3-dehydro-L-gulonate 6-phosphate + H⁺ = L-xylulose 5-phosphate + CO2

3-dehydro-L-gulonate 6-phosphate + H(+) = L-xylulose 5-phosphate + CO2 (Bound ligand (Het Group name = TX4) matches with 75.00% similarity)

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi0497392

Biochemistry 43:6438-6446 (2004)

PubMed id: 15157078

Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase.

E.L.Wise, W.S.Yew, J.A.Gerlt, I.Rayment.

ABSTRACT

3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC), a member of the orotidine monophosphate decarboxylase (OMPDC) suprafamily, catalyzes the Mg(2+)-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose 5-phosphate. Structural and biochemical evidence suggests that the KGPDC reaction proceeds via a Mg(2+)-stabilized 1,2-cis-enediolate intermediate. Protonation of the enediolate intermediate occurs in a nonstereospecific manner to form L-xylulose 5-phosphate. Although the exact mechanism of proton delivery is not known, Glu112, His136, and Arg139 have been implicated in this process [Yew, W. S., Wise, E., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 43, 6427-6437]. Surprisingly, single amino acid substitutions of these positions do not substantially reduce catalytic activity but rather alter the stereochemical course of the reaction. Here, we report the X-ray crystal structures of four mutants, K64A, H136A, E112Q, and E112Q/H136A, each determined in the presence of L-threonohydroxamate 4-phosphate, an analogue of the enediolate intermediate, to 1.7, 1.9, 1.8, and 1.9 A resolution, respectively. These structures reveal that substitutions of Lys64, Glu112, and His136 cause changes in the positions of the intermediate analogue and two active site water molecules that were previously identified as possible proton donors. These changes correlate with the observed alterations in the reaction stereochemistry for these mutants, thereby supporting a reaction mechanism in which water molecules competitively shuttle protons from the side chains of His136 and Arg139 to alternate faces of the cis-enediolate intermediate. These studies further underscore the wide variation in the reaction mechanisms in the OMPDC suprafamily.