2VZZ | pdb_00002vzz

Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb2VZZ/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-08-07 Released: 2009-04-07 
• Deposition Author(s): Vetting, M.W., Errey, J.C., Blanchard, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Rv0802C from Mycobacterium Tuberculosis: The First Structure of a Succinyltransferase with the Gnat Fold.

Vetting, M.W., Errey, J.C., Blanchard, J.S.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 978

• PubMed: 18997321 
• DOI: https://doi.org/10.1107/S1744309108031679
• Primary Citation Related Structures: 
  2VZY, 2VZZ


• PubMed Abstract: 
  

  Gene rv0802c from Mycobacterium tuberculosis encodes a 218-amino-acid protein and is annotated as a hypothetical protein with homology to GCN5-related N-acetyltransferases. The structure of Rv0802c was determined in an unliganded form to 2.0 A resolution utilizing single-wavelength anomalous dispersion from a samarium soak that resulted in a single bound Sm(3+):citrate(2) complex. The structure confirms that Rv0802c exhibits the GCN5-related N-acetyltransferase fold and revealed a tetramer composed of a dimer of dimers with approximate 222 symmetry. In addition, a bound acetate ion indicated that Rv0802c may utilize a unique acyl donor for the family. The subsequent determination of the structure of Rv0802c in complex with succinyl-CoA to 2.3 A resolution suggests that Rv0802c is the first known GCN5-related N-acetyltransferase family member to utilize succinyl-CoA as a substrate.

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Organizational Affiliation: 
• Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 103.53 kDa 
• Atom Count: 7,396 
• Modeled Residue Count: 843 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RV0802C	A, B, C, D	218	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 2.8.1
UniProt
Find proteins for P9WQG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQG7  Go to UniProtKB:  P9WQG7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCA	E [auth A], F [auth B], G [auth C], H [auth D]	SUCCINYL-COENZYME A C25 H40 N7 O19 P3 S VNOYUJKHFWYWIR-ITIYDSSPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.165	α = 90
b = 135.172	β = 90
c = 164.077	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Vetting, M.W., Errey, J.C., Blanchard, J.S.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description