4JDY

Crystal structure of Rv2606c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase

Kim, S.Kim, K.-J.

(2013) Biochem Biophys Res Commun 

  • DOI: 10.1016/j.bbrc.2013.04.068
  • Primary Citation of Related Structures:  
    4JDY

  • PubMed Abstract: 
  • Tuberculosis is a lethal infectious disease caused by Mycobacterium tuberculosis. We determined the crystal structure of Rv2606c, a potential pyridoxal biosynthesis lyase (PdxS), from M. tuberculosis H37Rv at 1.8 Å resolution. The overall structure o ...

    Tuberculosis is a lethal infectious disease caused by Mycobacterium tuberculosis. We determined the crystal structure of Rv2606c, a potential pyridoxal biosynthesis lyase (PdxS), from M. tuberculosis H37Rv at 1.8 Å resolution. The overall structure of the protein, composed of a (β/α)8-barrel and two small 310-helices, was quite similar to those of other PdxS proteins. A glycerol molecule was observed to be bound at the active site of the Rv2606c structure through interactions with the conserved residues of Asp29 and Lys86, providing information regarding the potential active site and the substrate-binding environment of the protein. The interface for Rv2606c dodecamerization, which is primarily mediated by salt bridges and hydrophobic interactions, was quite different from those of other PdxS proteins. Furthermore, we observed that the Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as PdxS and PdxT in M. tuberculosis.


    Organizational Affiliation

    School of Life Science and Biotechnology, Kyungpook National University, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyridoxal biosynthesis lyase PdxSABC264Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pdxSRv2606cMT2681MTCY1A10.27
EC: 4.3.3.6
Find proteins for P9WII9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WII9 
Go to UniProtKB:  P9WII9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.752α = 90
b = 126.08β = 90
c = 180.816γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-02-25 
  • Released Date: 2013-05-22 
  • Deposition Author(s): Kim, S., Kim, K.-J.

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description