PDBsum entry 1kgo

Metal binding protein

PDB id: 1kgo

Contents

Protein chains

296 a.a. *

Metals

FE2 ×8

Waters ×848

* Residue conservation analysis

PDB id:

1kgo

Name:

Metal binding protein

Title:

R2f from corynebacterium ammoniagenes in its reduced, fe containing, form

Structure:

Ribonucleotide reductase protein r2f. Chain: a, b, c, d. Engineered: yes

Source:

Corynebacterium ammoniagenes. Organism_taxid: 1697. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.25Å R-factor: 0.163 R-free: 0.238

Authors:

M.Hogbom,Y.Huque,B.M.Sjoberg,P.Nordlund

Key ref:

M.Högbom et al. (2002). Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes. Biochemistry, 41, 1381-1389. PubMed id: 11802741 DOI: 10.1021/bi011429l

Date:

28-Nov-01 Release date: 21-Dec-01

Protein chains

O69274  (O69274_CORAM) -  Ribonucleoside-diphosphate reductase subunit beta from Corynebacterium ammoniagenes

Seq: 329 a.a.

Struc: 296 a.a.

Enzyme reactions

• Enzyme class: E.C.1.17.4.1 - ribonucleoside-diphosphate reductase.
• Reaction: a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]-disulfide + H2O = a ribonucleoside 5'-diphosphate + [thioredoxin]-dithiol
• Cofactor: Fe(3+) or adenosylcob(III)alamin or Mn(2+)

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

reference

DOI no: 10.1021/bi011429l

Biochemistry 41:1381-1389 (2002)

PubMed id: 11802741

Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes.

M.Högbom, Y.Huque, B.M.Sjöberg, P.Nordlund.

ABSTRACT

Ribonucleotide reductase (RNR) is the enzyme performing de novo production of the four deoxyribonucleotides needed for DNA synthesis. All mammals as well as some prokaryotes express the class I enzyme which is an alpha(2)beta(2) protein. The smaller of the homodimers, denoted R2, contains a di-iron carboxylate site which, upon reaction with molecular oxygen, generates a stable tyrosyl radical needed for catalysis. The three-dimensional structure of the oxidized class Ib RNR R2 from Corynebacterium ammoniagenes has been determined at 1.85 A resolution and refined to an R-value of 15.8% (R(free) = 21.3%). In addition, structures of both the reduced iron-containing, and manganese-substituted protein have been solved. The C. ammoniagenes R2 has been proposed to be manganese-dependent. The present structure provides evidence that manganese is not oxidized by the protein, in agreement with recent biochemical data, and that no obvious structural abnormalities are seen in the oxidized and reduced iron-containing forms, giving further support that the protein is indeed an iron-dependent RNR R2. The di-manganese structure also provides an explanation for the magnetic properties of this site. The structure of the oxidized C. ammoniagenes R2 also reveals an additional water molecule bridging the radical and the iron site, which has not previously been seen in any other R2 structure and which might have important mechanistic implications.