2VZY

Crystal structure of Rv0802c from Mycobacterium tuberculosis in an unliganded form.

PDB DOI: https://doi.org/10.2210/pdb2VZY/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.205
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309108031679
Primary Citation of 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.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. vetting@aecom.yu.edu

Macromolecule Content

Total Structure Weight: 101.66 kDa
Atom Count: 6,823
Modelled Residue Count: 763
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RV0802C	A, B, C, D	218	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for P9WQG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQG7 Go to UniProtKB: P9WQG7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WQG7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D]	Q [auth D], R [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain Q [auth D] Focus chain R [auth D]
SM Query on SM Download Ideal Coordinates CCD File SDF format, chain T [auth D] MOL2 format, chain T [auth D]	T [auth D]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N		Interactions Focus chain T [auth D] Interactions & Density Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D]	F [auth A], I [auth B], L [auth C], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
ETX Query on ETX Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D]	G [auth A], J [auth B], M [auth C], N [auth C], S [auth D]	2-ETHOXYETHANOL C₄ H₁₀ O₂ ZNQVEEAIQZEUHB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain S [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D]	E [auth A], H [auth B], K [auth C], O [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]