PDBsum entry: 1uzr

Reductase

PDB id: 1uzr

Contents

Protein chains

282 a.a. *

Ligands

CIT ×3

GOL ×3

Metals

_FE ×6

Waters ×391

* Residue conservation analysis

PDB id:

1uzr

Name:

Reductase

Title:

Crystal structure of the class ib ribonucleotide reductase r2f-2 subunit from mycobacterium tuberculosis

Structure:

Ribonucleotide reductase r2-2 small subunit. Chain: a, b, c. Fragment: radical generating subunit, residues 1-296. Synonym: ribonucleotide reductase, ribonucleoside- diphosphate reductase r2-2, beta subunit. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.2Å R-factor: 0.177 R-free: 0.202

Authors:

M.Uppsten,J.Davis,H.Rubin,U.Uhlin

Key ref:

M.Uppsten et al. (2004). Crystal structure of the biologically active form of class Ib ribonucleotide reductase small subunit from Mycobacterium tuberculosis. FEBS Lett, 569, 117-122. PubMed id: 15225619 DOI: 10.1016/j.febslet.2004.05.059

Date:

15-Mar-04 Release date: 08-Jul-04

Protein chains

Q50549  (RIR2B_MYCTU) -  Ribonucleoside-diphosphate reductase subunit beta nrdF2

Seq: 324 a.a.

Struc: 282 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.17.4.1 - Ribonucleoside-diphosphate reductase.
• Reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H₂O = ribonucleoside diphosphate + thioredoxin
• Cofactor: Iron

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

 Gene Ontology (GO) functional annotation 

• Cellular component: ribonucleoside-diphosphate reductase complex (1 term)
• Biological process: growth (5 terms)
• Biochemical function: protein binding (5 terms)

reference

DOI no: 10.1016/j.febslet.2004.05.059

FEBS Lett 569:117-122 (2004)

PubMed id: 15225619

Crystal structure of the biologically active form of class Ib ribonucleotide reductase small subunit from Mycobacterium tuberculosis.

M.Uppsten, J.Davis, H.Rubin, U.Uhlin.

ABSTRACT

Two nrdF genes of Mycobacterium tuberculosis code for different R2 subunits of the class Ib ribonucleotide reductase (RNR). The proteins are denoted R2F-1 and R2F-2 having 71% sequence identity. The R2F-2 subunit forms the biologically active RNR complex with the catalytic R1E-subunit. We present the structure of the reduced R2F-2 subunit to 2.2 A resolution. Comparison of the R2F-2 structure with a model of R2F-1 suggests that the important differences are located at the C-terminus. We found that within class Ib, the E-helix close to the iron diiron centre has two preferred conformations, which cannot be explained by the redox-state of the diiron centre. In the R2F-2 structure, we also could see a mobility of alphaE in between the two conformations.

Selected figure(s)

Figure 1.
Fig. 1. Structure of Mycobacterium tuberculosis R2F-2 dimer. The subunits are coloured in beige and red, respectively, and the irons in the metal centre are shown as yellow spheres. Figs. 1, 2 and 4 were prepared using PyMOL [55].

Figure 3.
Fig. 3. Comparison of reduced and oxidised diiron centres. (a) Schematic picture of the reduced diiron site in Mtb R2F-2. (b) Crystallographic structure of the reduced diiron site in R2F-2 from Mtb. The iron coordination is identical to the one in the reduced S. typhimurium R2F (numbering in parenthesis). Final F[o]–F[c] map is contoured at 3σ where the iron ligating Glu197 was excluded from the calculation. (c) Structure of the oxidised diiron centre in S. typhimurium. (a) was made using MDL^®ISIS/Draw. (b) and (c) were made using Swiss-Pdb Viewer [56] (official URL, http://expasy.org/spdbv) and rendered with POV-Ray (official URL, http://www.povray.org).

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 569, 117-122) copyright 2004.

Figures were selected by an automated process.