1F8X

CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE

PDB DOI: https://doi.org/10.2210/pdb1F8X/pdb

Classification: TRANSFERASE
Organism(s): Lactobacillus leichmannii
Mutation(s): No

Deposited: 2000-07-05 Released: 2000-07-26
Deposition Author(s): Armstrong, S.R., Cook, W.J., Short, S.A., Ealick, S.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.240
R-Value Work: 0.166

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.

Armstrong, S.R., Cook, W.J., Short, S.A., Ealick, S.E.

(1996) Structure 4: 97-107

PubMed: 8805514 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(96)00013-5
Primary Citation of Related Structures:
1F8X, 1F8Y

PubMed Abstract:
Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. The kinetics describe a ping-pong-bi-bi pathway involving the formation of a covalent enzyme-deoxyribose intermediate. The enzyme is produced by a limited number of microorganisms and its functions have been exploited in its use as a biocatalyst to synthesize nucleoside analogs of therapeutic interest.

Organizational Affiliation

Section of Biochemistry, Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.

Macromolecule Content

Total Structure Weight: 36.2 kDa
Atom Count: 2,616
Modelled Residue Count: 312
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE	A, B	157	Lactobacillus leichmannii	Mutation(s): 0 EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii) Explore Q9R5V5 Go to UniProtKB: Q9R5V5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R5V5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.240
R-Value Work: 0.166
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151	α = 90
b = 151	β = 90
c = 151	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
SDMS	data reduction
SDMS	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2000-07-26

Deposition Author(s):

Armstrong, S.R.

Revision History (Full details and data files)

Version 1.0: 2000-07-26
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.