PDBsum entry: 2h89

Oxidoreductase

PDB-id: 2h89

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

Main view

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

613 a.a. *

241 a.a. *

139 a.a. *

102 a.a. *

Ligands

FAD

MLI

UNL ×40

FES

SF4

F3S

BHG

HEM

PEE ×2

Metal ions

__K ×2

Waters ×580

* Residue conservation analysis

Tools

Clefts Calculation

Bottom view	Right view

PDB id:

2h89

Name:

Oxidoreductase

Title:

Avian respiratory complex ii with malonate bound

Structure:

Succinate dehydrogenase flavoprotein subunit. Chain: a. Succinate dehydrogenase ip subunit. Chain: b. Succinate dehydrogenase cytochrome b, large subunit. Chain: c. Succinate dehydrogenase cytochrome b, small subunit.

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Organism_taxid: 9031

Biological unit:

Tetramer (from PQS)

UniProt:

Chain A: Q9YHT1 (DHSA_CHICK)

Seq:
Struc:
	Seq:
	Struc:
Seq:		665 a.a.
Struc:		613 a.a.*

Chain B: Q9YHT2 (DHSB_CHICK)

Seq:
Struc:
	Seq:	290 a.a.
	Struc:	241 a.a.

Chain D: Q5ZIS0 (DHSD_CHICK)

Seq:

157 a.a.

Struc:

102 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme class:

Chains A, B: E.C.1.3.5.1   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Succinate + ubiquinone = fumarate + ubiquinol (see diagram below)

Cofactor:

FAD; Iron-sulfur

Pathway:

Citric acid cycle

Resolution:

2.40Å

R-factor:

0.226

R-free:

0.279

Authors:

L.S.Huang,J.T.Shen,A.C.Wang,E.A.Berry

Key ref:

L.S.Huang et al. (2006). Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.. Biochim Biophys Acta, 1757, 1073-1083. [PubMed id: 16935256] [DOI: 10.1016/j.bbabio.2006.06.015]

Date:

06-Jun-06

Release date:

20-Jun-06

Related entries:

2fbw
avian complex ii with carboxin bound
1yq3
avian complex ii from orthorhombic crystal form
1yq4
avian complex ii, 3-nitropropionic acid-modified
1zoy
porcine complex ii from orthorhombic crystal
1zp0
porcine complex ii with 3-nitropropionate and ttfa bound

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1016/j.bbabio.2006.06.015

Biochim Biophys Acta 1757:1073-1083 (2006)

PubMed id: 16935256

Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.

L.S.Huang, J.T.Shen, A.C.Wang, E.A.Berry.

ABSTRACT

Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We crystallized Complex II in the presence of oxaloacetate or with the endogenous inhibitor bound. The structure showed a ligand essentially identical to the "malate-like intermediate" found in Shewanella Flavocytochrome c crystallized with fumarate (P. Taylor, et al., Nat. Struct. Biol. 6 1108-1112) Crystallization of Complex II in the presence of excess fumarate also gave the malate-like intermediate or a mixture of that and fumarate at the active site. In order to more conveniently monitor the occupation state of the dicarboxylate site, we are developing a library of UV/Vis spectral effects induced by binding different ligands to the site. Treatment with fumarate results in rapid development of the fumarate difference spectrum and then a very slow conversion into a species spectrally similar to the OAA-liganded complex. Complex II is known to be capable of oxidizing malate to the enol form of oxaloacetate (Y.O. Belikova, et al., Biochim. Biophys. Acta 936 1-9). The observations above suggest it may also be capable of interconverting fumarate and malate. It may be useful for understanding the mechanism and regulation of the enzyme to identify the malate-like intermediate and its pathway of formation from oxaloacetate or fumarate.