PDBsum entry 2eb5

Lyase

PDB id: 2eb5

Contents

Protein chains

259 a.a. *

Ligands

OXL ×5

SCN ×7

Metals

_MG ×5

Waters ×755

* Residue conservation analysis

PDB id:

2eb5

Name:

Lyase

Title:

Crystal structure of hpcg complexed with oxalate

Structure:

2-oxo-hept-3-ene-1,7-dioate hydratase. Chain: a, b, c, d, e. Synonym: 2-oxo-hept-4-ene-1,7-dioate hydratase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: strain c. Gene: hpcg. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.194 R-free: 0.226

Authors:

A.Izumi,D.Rea,T.Adachi,S.Unzai,S.Y.Park,D.I.Roper,J.R.H.Tame

Key ref:

A.Izumi et al. (2007). Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli. J Mol Biol, 370, 899-911. PubMed id: 17559873 DOI: 10.1016/j.jmb.2007.05.006

Date:

07-Feb-07 Release date: 17-Jul-07

Protein chains

Q46982  (Q46982_ECOLX) -  2-hydroxyhexa-2,4-dienoate hydratase from Escherichia coli

Seq: 267 a.a.

Struc: 259 a.a.

Enzyme reactions

• Enzyme class 2: E.C.4.1.1.77 - 2-oxo-3-hexenedioate decarboxylase.
• Reaction: (3E)-2-oxohex-3-enedioate + H⁺ = 2-oxopent-4-enoate + CO2

(3E)-2-oxohex-3-enedioate + H(+) = 2-oxopent-4-enoate (Bound ligand (Het Group name = OXL) matches with 55.56% similarity) + CO2

• Enzyme class 3: E.C.4.2.1.132 - 2-hydroxyhexa-2,4-dienoate hydratase.
• Reaction: (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + H2O = 4-hydroxy-2-oxohexanoate

(2Z,4Z)-2-hydroxyhexa-2,4-dienoate + H2O = 4-hydroxy-2-oxohexanoate (Bound ligand (Het Group name = OXL) matches with 45.45% similarity)

• Enzyme class 4: E.C.4.2.1.80 - 2-oxopent-4-enoate hydratase.
• Reaction: (S)-4-hydroxy-2-oxopentanoate = (2Z)-2-hydroxypenta-2,4-dienoate + H2O

4-hydroxy-2-oxopentanoate = 2-oxopent-4-enoate (Bound ligand (Het Group name = OXL) matches with 55.56% similarity) + H(2)O

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.jmb.2007.05.006

J Mol Biol 370:899-911 (2007)

PubMed id: 17559873

Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli.

A.Izumi, D.Rea, T.Adachi, S.Unzai, S.Y.Park, D.I.Roper, J.R.Tame.

ABSTRACT

HpcG catalyses the hydration of a carbon-carbon double bond without the aid of any cofactor other than a simple divalent metal ion such as Mg(2+). Since the substrate has a nearby carbonyl group, it is believed that it first isomerises to form a pair of conjugated double bonds in the enol tautomer before Michael addition of water. Previous chemical studies of the reaction, and that of the related enzyme MhpD, have failed to provide a clear picture of the mechanism. The substrate itself is unstable, preventing co-crystallisation or soaking of crystals, but oxalate is a strong competitive inhibitor. We have solved the crystal structure of the protein in the apo form, and with magnesium and oxalate bound. Modelling substrate into the active site suggests the attacking water molecule is not part of the metal coordination shell, in contrast to a previous proposal. Our model suggests that geometrically strained cis isomer intermediates do not lie on the reaction pathway, and that separate groups are involved in the isomerisation and hydration steps.

Selected figure(s)

Figure 2.
Figure 2. (a) The five HpcG monomers in the asymmetric unit, coloured by chain. (b) The HpcG decamer, coloured by pentamer ring.

Figure 7.
Figure 7. The active site of HpcG with oxalate and magnesium ion bound. Water molecules are shown as blue spheres, and the magnesium ion as a red sphere. Atomic distances less than 3.2 Å are shown with dotted lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 899-911) copyright 2007.

Figures were selected by an automated process.