2X9Q

Structure of the Mycobacterium tuberculosis protein, Rv2275, demonstrates that cyclodipeptide synthetases are related to type I tRNA-Synthetases.

PDB DOI: https://doi.org/10.2210/pdb2X9Q/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-23 Released: 2010-09-22
Deposition Author(s): Vetting, M.W., Hegde, S.S., Blanchard, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.210
R-Value Work: 0.180
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Structure and Mechanism of the Mycobacterium Tuberculosis Cyclodityrosine Synthetase.

Vetting, M.W., Hegde, S.S., Blanchard, J.S.

(2010) Nat Chem Biol 6: 797

PubMed: 20852636 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nchembio.440
Primary Citation of Related Structures:
2X9Q

PubMed Abstract:
The Mycobacterium tuberculosis enzyme Rv2275 catalyzes the formation of cyclo(L-Tyr-L-Tyr) using two molecules of Tyr-tRNA(Tyr) as substrates. The three-dimensional (3D) structure of Rv2275 was determined to 2.0-Å resolution, revealing that Rv2275 is structurally related to the class Ic aminoacyl-tRNA synthetase family of enzymes. Mutagenesis and radioactive labeling suggests a covalent intermediate in which L-tyrosine is transferred from Tyr-tRNA(Tyr) to an active site serine (Ser88) by transesterification with Glu233 serving as a critical base, catalyzing dipeptide bond formation.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.

Macromolecule Content

Total Structure Weight: 63.8 kDa
Atom Count: 3,804
Modelled Residue Count: 453
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLODIPEPTIDE SYNTHETASE	A, B	289	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for P9WPF9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPF9 Go to UniProtKB: P9WPF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.210
R-Value Work: 0.180
R-Value Observed: 0.181
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.09	α = 90
b = 75.06	β = 90
c = 140.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Blanchard, J.S.

Revision History (Full details and data files)

Version 1.0: 2010-09-22
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

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.