2X9Q | pdb_00002x9q

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.210 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2X9Q

This is version 1.3 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

  • DOI: https://doi.org/10.1038/nchembio.440
  • Primary Citation 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 
  • Modeled Residue Count: 453 
  • Deposited Residue Count: 578 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYCLODIPEPTIDE SYNTHETASE
A, B
289Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 2.3.2.21
UniProt
Find proteins for P9WPF9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPF9 
Go to UniProtKB:  P9WPF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPF9
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.210 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.09α = 90
b = 75.06β = 90
c = 140.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

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
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary