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PDBsum entry 2yvk

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Isomerase PDB id
2yvk
Jmol
Contents
Protein chains
349 a.a. *
Ligands
MRU ×4
Waters ×250
* Residue conservation analysis
PDB id:
2yvk
Name: Isomerase
Title: Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from bacillus subtilis
Structure: Methylthioribose-1-phosphate isomerase. Chain: a, b, c, d. Synonym: mtr-1-p isomerase, s-methyl-5-thioribose-1- phosphate isomerase. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: mtna. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.40Å     R-factor:   0.212     R-free:   0.257
Authors: H.Tamura,T.Inoue,Y.Kai,H.Matsumura
Key ref:
H.Tamura et al. (2008). Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism. Protein Sci, 17, 126-135. PubMed id: 18156470 DOI: 10.1110/ps.073169008
Date:
13-Apr-07     Release date:   22-Jan-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O31662  (MTNA_BACSU) -  Methylthioribose-1-phosphate isomerase
Seq:
Struc:
353 a.a.
349 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.23  - S-methyl-5-thioribose-1-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate
S-methyl-5-thio-alpha-D-ribose 1-phosphate
Bound ligand (Het Group name = MRU)
corresponds exactly
= S-methyl-5-thio-D-ribulose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cellular metabolic process   6 terms 
  Biochemical function     isomerase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1110/ps.073169008 Protein Sci 17:126-135 (2008)
PubMed id: 18156470  
 
 
Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism.
H.Tamura, Y.Saito, H.Ashida, T.Inoue, Y.Kai, A.Yokota, H.Matsumura.
 
  ABSTRACT  
 
The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Structural comparison of Bs-M1Pi with Af-M1PiRP. Molecular
Figure 6.
Figure 6. Proposed reaction mechanisms of M1Pi. (A) Substrate MTR-1-P-binding model of Bs-M1Pi in the active site. (Orange
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2008, 17, 126-135) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19946895 E.Albers (2009).
Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine.
  IUBMB Life, 61, 1132-1142.  
19620624 Y.Kabuyama, E.S.Litman, P.D.Templeton, S.I.Metzner, E.S.Witze, G.M.Argast, S.J.Langer, K.Polvinen, Y.Shellman, D.Chan, J.B.Shabb, J.E.Fitzpatrick, K.A.Resing, M.C.Sousa, and N.G.Ahn (2009).
A mediator of Rho-dependent invasion moonlights as a methionine salvage enzyme.
  Mol Cell Proteomics, 8, 2308-2320.  
19279009 Y.Saito, H.Ashida, T.Sakiyama, N.T.de Marsac, A.Danchin, A.Sekowska, and A.Yokota (2009).
Structural and functional similarities between a ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Bacillus subtilis and photosynthetic RuBisCO.
  J Biol Chem, 284, 13256-13264.  
19101471 H.Deng, S.M.Cross, R.P.McGlinchey, J.T.Hamilton, and D.O'Hagan (2008).
In vitro reconstituted biotransformation of 4-fluorothreonine from fluoride ion: application of the fluorinase.
  Chem Biol, 15, 1268-1276.  
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.