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PDBsum entry 1rfm

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1rfm
Jmol PyMol
Contents
Protein chains
(+ 2 more) 344 a.a. *
Ligands
NAD ×8
Waters ×506
* Residue conservation analysis
Superseded by: 2x06
PDB id:
1rfm
Name: Oxidoreductase
Title: Sulfolactate dehydrogenase from methanocaldococcus jannaschii
Structure: L-sulfolactate dehydrogenase. Chain: a, b, c, d, e, f, g, h. Fragment: sulfolactate dehydrogenase. Synonym: r, -sulfolactate dehydrogenase, r, -2-hydroxyacid dehydrogenase. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: comc, mdh, mj1425. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.199     R-free:   0.243
Authors: A.Irimia,D.Madern,G.Zaccai,F.M.D.Vellieux
Key ref:
A.Irimia et al. (2004). Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes. EMBO J, 23, 1234-1244. PubMed id: 15014443 DOI: 10.1038/sj.emboj.7600147
Date:
10-Nov-03     Release date:   16-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58820  (COMC_METJA) -  L-sulfolactate dehydrogenase
Seq:
Struc:
344 a.a.
344 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.272  - D-2-hydroxyacid dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An (R)-2-hydroxycarboxylate + NADP+ = a 2-oxocarboxylate + NADPH
(R)-2-hydroxycarboxylate
+
NADP(+)
Bound ligand (Het Group name = NAD)
matches with 91.00% similarity
= 2-oxocarboxylate
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/sj.emboj.7600147 EMBO J 23:1234-1244 (2004)
PubMed id: 15014443  
 
 
Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes.
A.Irimia, D.Madern, G.Zaccaï, F.M.Vellieux.
 
  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 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.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Active site of MjSLDH. (A) The NADH cofactor is shown in sticks inside the final omit map (magenta chicken wire) contoured at 1.0 . The residues involved in cofactor binding, and the presumed residues of the catalytic site are labelled, with an indication of their subunit of origin. Broken lines represent the hydrogen bonds between cofactor atoms and those of the protein. A stereo version of this figure is available as Supplementary Figure 2S. (B) Close-up view of the active site in monomer A. Monomers A and B are colored in red and mauve, respectively, except for the mobile domain of monomer A, which is shown in cyan. The NADH and several potential active site residues are shown in stick representation. (C) Schematic representation of the active site. Hydrogen bonds are represented by thick dashed lines, while thin dashed lines show the interaction of T156A with the C4 and C5 atoms of the nicotinamide ring of NADH.
Figure 3.
Figure 3 Comparison of the glycine-rich motif in the 3-D structure of MjSLDH to the 'classical' motif present in dehydrogenases with a Rossman-fold motif. Hydrogen bonds between cofactor and protein are shown by dashed lines. (A) Stereo view of NADH interacting at the level of the diphosphate moiety with residue K225 in the glycine-rich motif of MjSLDH. This glycine-rich sequence signature is located at the amino-terminal end of helix H. (B) Stereo view of NAD interacting with the glycine-rich motif found in a representative member of Rossman-fold dehydrogenases, the (R207S, R292S) mutant of HmMalDH (PDB id. 1O6Z; Irimia et al, 2003).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1234-1244) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20007648 K.Denger, and A.M.Cook (2010).
Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase.
  Microbiology, 156, 967-974.  
17890343 K.R.Hristova, R.Schmidt, A.Y.Chakicherla, T.C.Legler, J.Wu, P.S.Chain, K.M.Scow, and S.R.Kane (2007).
Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol.
  Appl Environ Microbiol, 73, 7347-7357.  
16233829 H.Muramatsu, H.Mihara, M.Goto, I.Miyahara, K.Hirotsu, T.Kurihara, and N.Esaki (2005).
A new family of NAD(P)H-dependent oxidoreductases distinct from conventional Rossmann-fold proteins.
  J Biosci Bioeng, 99, 541-547.  
15561717 H.Muramatsu, H.Mihara, R.Kakutani, M.Yasuda, M.Ueda, T.Kurihara, and N.Esaki (2005).
The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent delta1-piperideine-2-carboxylate/delta1-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline.
  J Biol Chem, 280, 5329-5335.  
16192274 M.Goto, H.Muramatsu, H.Mihara, T.Kurihara, N.Esaki, R.Omi, I.Miyahara, and K.Hirotsu (2005).
Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction.
  J Biol Chem, 280, 40875-40884.
PDB codes: 1wtj 2cwf 2cwh
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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