2X06

SULFOLACTATE DEHYDROGENASE FROM METHANOCALDOCOCCUS JANNASCHII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Methanoarchaeal Sulfolactate Dehydrogenase: Prototype of a New Family of Nadh-Dependent Enzymes.

Irimia, A.Madern, D.Vellieux, F.M.D.

(2004) Embo J. 23: 1234

  • DOI: 10.1038/sj.emboj.7600147
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of the sulfolactate dehydrogenase from the hyperthermophilic and methanogenic archaeon Methanocaldococcus jannaschii was solved at 2.5 A resolution (PDB id. 1RFM). The asymmetric unit contains a tetramer of tight dimers. This st ...

    The crystal structure of the sulfolactate dehydrogenase from the hyperthermophilic and methanogenic archaeon Methanocaldococcus jannaschii was solved at 2.5 A resolution (PDB id. 1RFM). The asymmetric unit contains a tetramer of tight dimers. This structure, complexed with NADH, does not contain a cofactor-binding domain with 'Rossmann-fold' topology. Instead, the tertiary and quaternary structures indicate a novel fold. The NADH is bound in an extended conformation in each active site, in a manner that explains the pro-S specificity. Cofactor binding involves residues belonging to both subunits within the tight dimers, which are therefore the smallest enzymatically active units. The protein was found to be a homodimer in solution by size-exclusion chromatography, analytical ultracentrifugation and small-angle neutron scattering. Various compounds were tested as putative substrates. The results indicate the existence of a substrate discrimination mechanism, which involves electrostatic interactions. Based on sequence homology and phylogenetic analyses, several other enzymes were classified as belonging to this novel family of homologous (S)-2-hydroxyacid dehydrogenases.


    Related Citations: 
    • The First Examples of (S)-2-Hydroxyacid Dehydrogenases Catalyzing the Transfer of the Pro-4S Hydrogen of Nadh are Found in the Archaea.
      Graupner, M.,White, R.H.
      (2001) Biochim.Biophys.Acta 1548: 169
    • Identification of an Archaeal 2-Hydroxy Acid Dehydrogenase Catalyzing Reactions Involved in Coenzyme Biosynthesis in Methanoarchaea.
      Graupner, M.,Xu, H.,White, R.H.
      (2000) J.Bacteriol. 182: 3688


    Organizational Affiliation

    Laboratoire de Biophysique Mol├ęculaire, Institut de Biologie Structurale J-P Ebel CEA CNRS UJF, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-SULFOLACTATE DEHYDROGENASE
A, B, C, D, E, F, G, H
344Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: comC (mdh)
EC: 1.1.1.337
Find proteins for Q58820 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.930α = 90.00
b = 203.710β = 112.05
c = 100.050γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MLPHAREphasing
SnBphasing
PHENIXrefinement
XDSdata reduction
TRUNCATEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Refinement description
  • Version 1.4: 2019-01-30
    Type: Data collection, Experimental preparation
  • Version 1.5: 2019-02-06
    Type: Data collection, Experimental preparation