3HYS

Structure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis.

Johnston, J.M.Jiang, M.Guo, Z.Baker, E.N.

(2010) Acta Crystallogr D Biol Crystallogr 66: 909-917

  • DOI: 10.1107/S0907444910025771
  • Primary Citation of Related Structures:  
    3E3A, 3HSS, 3HYS

  • PubMed Abstract: 
  • Mycobacterium tuberculosis, the cause of tuberculosis, is a devastating human pathogen against which new drugs are urgently needed. Enzymes from the biosynthetic pathway for menaquinone are considered to be valid drug targets. The protein encoded by the open reading frame Rv0554 has been expressed, purified and subjected to structural and functional analysis to test for a putative role in menaquinone biosynthesis ...

    Mycobacterium tuberculosis, the cause of tuberculosis, is a devastating human pathogen against which new drugs are urgently needed. Enzymes from the biosynthetic pathway for menaquinone are considered to be valid drug targets. The protein encoded by the open reading frame Rv0554 has been expressed, purified and subjected to structural and functional analysis to test for a putative role in menaquinone biosynthesis. The crystal structure of Rv0554 has been solved and refined in two different space groups at 2.35 and 1.9 A resolution. The protein is dimeric, with an alpha/beta-hydrolase monomer fold. In each monomer, a large cavity adjacent to the catalytic triad is enclosed by a helical lid. Dimerization is mediated by the lid regions. Small-molecule additives used in crystallization bind in the active site, but no binding of ligands related to menaquinone biosynthesis could be detected and functional assays failed to support possible roles in menaquinone biosynthesis.


    Organizational Affiliation

    School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
protein Rv0554, putative BromoperoxidaseA, B293Mycobacterium tuberculosisMutation(s): 0 
Gene Names: bpoCMT0580Rv0554
EC: 1.11.1
UniProt
Find proteins for P9WNH1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNH1 
Go to UniProtKB:  P9WNH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNH1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MLA
Query on MLA

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.435α = 90
b = 100.435β = 90
c = 135.064γ = 90
Software Package:
Software NamePurpose
HKLdata processing
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKLdata reduction
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description