PDBsum entry 3itt

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Isomerase, metal-binding protein PDB id
Protein chains
421 a.a. *
RNS ×4
_MN ×8
Waters ×1259
* Residue conservation analysis
PDB id:
Name: Isomerase, metal-binding protein
Title: Crystal structure of pseudomonas stutzeri l-rhamnose isomerase mutant s329k in complex with l-rhamnose
Structure: L-rhamnose isomerase. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Pseudomonas stutzeri. Pseudomonas perfectomarina. Organism_taxid: 316. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.96Å     R-factor:   0.183     R-free:   0.225
Authors: H.Yoshida,M.Yamaji,T.Ishii,K.Izumori,S.Kamitori
Key ref: H.Yoshida et al. (2010). Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures. FEBS J, 277, 1045-1057. PubMed id: 20088877
28-Aug-09     Release date:   02-Feb-10    
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Protein chains
Pfam   ArchSchema ?
Q75WH8  (Q75WH8_PSEST) -  L-rhamnose isomerase
430 a.a.
421 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     isomerase activity     2 terms  


FEBS J 277:1045-1057 (2010)
PubMed id: 20088877  
Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures.
H.Yoshida, M.Yamaji, T.Ishii, K.Izumori, S.Kamitori.
L-Rhamnose isomerase (L-RhI) catalyzes the reversible isomerization of L-rhamnose to L-rhamnulose. Pseudomonas stutzeril-RhI, with a broad substrate specificity, can catalyze not only the isomerization of L-rhamnose, but also that between D-allose and D-psicose. For the aldose-ketose isomerization by L-RhI, a metal-mediated hydride-shift mechanism has been proposed, but the catalytic mechanism is still not entirely understood. To elucidate the entire reaction mechanism, the X-ray structures of P. stutzeril-RhI in an Mn(2+)-bound form, and of two inactive mutant forms of P. stutzeril-RhI (S329K and D327N) in a complex with substrate/product, were determined. The structure of the Mn(2+)-bound enzyme indicated that the catalytic site interconverts between two forms with the displacement of the metal ion to recognize both pyranose and furanose ring substrates. Solving the structures of S329K-substrates allowed us to examine the metal-mediated hydride-shift mechanism of L-RhI in detail. The structural analysis of D327N-substrates and additional modeling revealed Asp327 to be responsible for the ring opening of furanose, and a water molecule coordinating with the metal ion to be involved in the ring opening of pyranose.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20977999 H.Yoshida, K.Takeda, K.Izumori, and S.Kamitori (2010).
Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of pseudomonas stutzeri L-rhamnose isomerase.
  Protein Eng Des Sel, 23, 919-927.
PDB codes: 3m0h 3m0l 3m0m 3m0v 3m0x 3m0y
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