PDBsum entry 4hk5

Lyase

PDB id: 4hk5

Contents

Protein chains

358 a.a.

380 a.a.

Metals

_ZN ×5

Waters ×931

PDB id:

4hk5

Name:

Lyase

Title:

Crystal structure of cordyceps militaris idcase in apo form

Structure:

Uracil-5-carboxylate decarboxylase. Chain: a, b, c, d. Synonym: idcase. Engineered: yes

Source:

Cordyceps militaris. Caterpillar fungus. Organism_taxid: 73501. Gene: ccm_01452. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.90Å R-factor: 0.159 R-free: 0.197

Authors:

S.Xu,J.Zhu,J.Ding

Key ref:

S.Xu et al. (2013). Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase. Cell Res, 23, 1296-1309. PubMed id: 23917530 DOI: 10.1038/cr.2013.107

Date:

15-Oct-12 Release date: 11-Sep-13

Protein chains

G3J531  (G3J531_CORMM) -  Uracil-5-carboxylate decarboxylase from Cordyceps militaris (strain CM01)

Seq: 376 a.a.

Struc: 358 a.a.

Protein chain

G3J531  (G3J531_CORMM) -  Uracil-5-carboxylate decarboxylase from Cordyceps militaris (strain CM01)

Seq: 376 a.a.

Struc: 380 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.4.1.1.66 - uracil-5-carboxylate decarboxylase.
• Reaction: uracil 5-carboxylate + H⁺ = uracil + CO2

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

reference

DOI no: 10.1038/cr.2013.107

Cell Res 23:1296-1309 (2013)

PubMed id: 23917530

Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase.

S.Xu, W.Li, J.Zhu, R.Wang, Z.Li, G.L.Xu, J.Ding.

ABSTRACT

DNA methylation and demethylation regulate many crucial biological processes in mammals and are linked to many diseases. Active DNA demethylation is believed to be catalyzed by TET proteins and a putative DNA decarboxylase that may share some similarities in sequence, structure and catalytic mechanism with isoorotate decarboxylase (IDCase) that catalyzes decarboxylation of 5caU to U in fungi. We report here the structures of wild-type and mutant IDCases from Cordyceps militaris and Metarhizium anisopliae in apo form or in complexes with 5caU, U, and an inhibitor 5-nitro-uracil. IDCases adopt a typical (β/α)8 barrel fold of the amidohydrolase superfamily and function as dimers. A Zn(2+) is bound at the active site and coordinated by four strictly conserved residues, one Asp and three His. The substrate is recognized by several strictly conserved residues. The functional roles of the key residues at the active site are validated by mutagenesis and biochemical studies. Based on the structural and biochemical data, we present for the first time a novel catalytic mechanism of decarboxylation for IDCases, which might also apply to other members of the amidohydrolase superfamily. In addition, our biochemical data show that IDCases can catalyze decarboxylation of 5caC to C albeit with weak activity, which is the first in vitro evidence for direct decarboxylation of 5caC to C by an enzyme. These findings are valuable in the identification of potential DNA decarboxylase in mammals.