PDBsum entry 3cb0

Oxidoreductase

PDB id: 3cb0

Contents

Protein chains

166 a.a. *

Ligands

FMN ×2

Waters ×1201

* Residue conservation analysis

PDB id:

3cb0

Name:

Oxidoreductase

Title:

Cobr

Structure:

4-hydroxyphenylacetate 3-monooxygenase. Chain: a, b, c, d. Synonym: cobr, corrin reductase. Engineered: yes

Source:

Brucella melitensis. Organism_taxid: 29459. Gene: cobr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.197 R-free: 0.231

Authors:

A.D.Lawrence,M.J.Warren,R.W.Pickersgill

Key ref:

A.D.Lawrence et al. (2008). Identification, characterization, and structure/function analysis of a corrin reductase involved in adenosylcobalamin biosynthesis. J Biol Chem, 283, 10813-10821. PubMed id: 18263579 DOI: 10.1074/jbc.M710431200

Date:

21-Feb-08 Release date: 11-Mar-08

Protein chains

Q8YHT7  (Q8YHT7_BRUME) -  4-hydroxyphenylacetate 3-monooxygenase from Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

Seq: 173 a.a.

Struc: 166 a.a.

Enzyme reactions

• Enzyme class: E.C.1.14.14.9 - 4-hydroxyphenylacetate 3-monooxygenase.
• Reaction: 4-hydroxyphenylacetate + FADH2 + O2 = 3,4-dihydroxyphenylacetate + FAD + H2O + H⁺

4-hydroxyphenylacetate + FADH2 (Bound ligand (Het Group name = FMN) matches with 58.49% similarity) + O2 = 3,4-dihydroxyphenylacetate + FAD + H2O + H(+)

• Cofactor: FAD

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

reference

DOI no: 10.1074/jbc.M710431200

J Biol Chem 283:10813-10821 (2008)

PubMed id: 18263579

Identification, characterization, and structure/function analysis of a corrin reductase involved in adenosylcobalamin biosynthesis.

A.D.Lawrence, E.Deery, K.J.McLean, A.W.Munro, R.W.Pickersgill, S.E.Rigby, M.J.Warren.

ABSTRACT

Vitamin B(12), the antipernicious anemia factor, is the cyano derivative of adenosylcobalamin, which is one of nature's most complex coenzymes. Adenosylcobalamin is made along one of two similar yet distinct metabolic pathways, which are referred to as the aerobic and anaerobic routes. The aerobic pathway for cobalamin biosynthesis proceeds via cobalt insertion into a ring-contracted macrocycle, which is closely followed by adenosylation of the cobalt ion. An important prerequisite for adenosylation is the reduction of the centrally chelated metal from Co(II) to a highly nucleophilic Co(I) form. We have cloned a gene, cobR, encoding a biosynthetic enzyme with this co(II)rrin reductase activity from Brucella melitensis. The protein has been overproduced, and the resulting flavoprotein has been purified, characterized, and crystallized and its structure determined to 1.6A resolution. Kinetic and EPR analysis reveals that the enzyme proceeds via a semiquinone form. It is proposed that CobR may interact with the adenosyltransferase to overcome the large thermodynamic barrier required for co(II)rrin reduction.

Selected figure(s)

Figure 1.
FIGURE 1. Biosynthesis of vitamin B[12], highlighting the transformation of cob(II)yrinic acid a,c-diamide into adenonsylcob(III)yrinic acid a,c-diamide. After the insertion of cobalt into the contracted ring system by CobNST, the central cobalt ion of cobyrinic acid a,c-diamide is reduced to the Co(I) form by CobR, which acts as a nucleophile for the adenosylation process.

Figure 6.
FIGURE 6. Crystal structure of CobR. a, schematic representation of the homodimer architecture of CobR with FMN shown in stick representation. The si face of the FMN is presented to the large central cavity. b, [A] weighted 2F[obs] - F[calc] Fourier synthesis showing the quality of the electron density corresponding to the isoalloxazine ring of the bound FMN; the electron density is contoured at 1 (blue mesh). c, schematic representation showing the superimposition of flavin reductase (Phe(A2)) and CobR, which brings the isoalloxazine rings of the flavins shown in stick representation into close structural alignment. The position of -helix 4 of CobR precludes the binding of adenosine at the corresponding position in CobR, and there is no adjacent binding pocket that can accommodate the adenosine. The NAD bound by flavin reductase can be readily accommodated in CobR. d, more detailed view of FMN and proposed NAD binding in CobR showing some key interactions with FMN and NAD. The measured distance between the modeled NAD (nicotinamide) C-5 and the experimentally observed isoalloxazine ring N-5 of 3.2 Å is consistent with hydride transfer from C-5 of NADH to N-5 of FMN. Produced using PyMol (17).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 10813-10821) copyright 2008.

Figures were selected by an automated process.