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Isomerase PDB id
1rii
Jmol
Contents
Protein chains
243 a.a. *
231 a.a. *
Ligands
GOL ×5
Waters ×451
* Residue conservation analysis
PDB id:
1rii
Name: Isomerase
Title: Crystal structure of phosphoglycerate mutase from m. Tubercu
Structure: 2,3-bisphosphoglycerate-dependent phosphoglycerat chain: a, b, c, d. Synonym: phosphoglyceromutase, pgam, bpg-dependent pgam, dp engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: gpma, gpm, pgm, gpm1, rv0489, mt0508, mtcy20g9.15, mb expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.221     R-free:   0.270
Authors: P.Mueller,M.R.Sawaya,S.Chan,Y.Wu,I.Pashkova,J.Perry,D.Eisenb Structural Genomics Consortium (Tbsgc)
Key ref:
P.Müller et al. (2005). The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase. Acta Crystallogr D Biol Crystallogr, 61, 309-315. PubMed id: 15735341 DOI: 10.1107/S0907444904033190
Date:
17-Nov-03     Release date:   05-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A5R6  (GPMA_MYCTU) -  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Seq:
Struc: 		249 a.a.
243 a.a.
Protein chain
Pfam   ArchSchema ?
P0A5R6  (GPMA_MYCTU) -  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Seq:
Struc: 		249 a.a.
231 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.5.4.2.1  - Phosphoglycerate mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
2-phospho-D-glycerate
Bound ligand (Het Group name = GOL)
matches with 54.55% similarity 		= 3-phospho-D-glycerate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444904033190 Acta Crystallogr D Biol Crystallogr 61:309-315 (2005)
PubMed id: 15735341  
 
 
The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.
P.Müller, M.R.Sawaya, I.Pashkov, S.Chan, C.Nguyen, Y.Wu, L.J.Perry, D.Eisenberg.
 
  ABSTRACT  
 
The single-crystal X-ray structure of phosphoglycerate mutase from Mycobacterium tuberculosis has been determined at a resolution of 1.70 angstroms. The C-terminal tail of each of the subunits is flexible and disordered; however, for one of the four chains (chain A) all but five residues of the chain could be modeled. Noteworthy features of the structure include the active site and a proline-rich segment in each monomer forming a short left-handed polyprolyl helix. These segments lie on the enzyme surface and could conceivably participate in protein-protein interactions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Homotetramer of M. tuberculosis phosphoglycerate mutase, possessing pseudo-222 symmetry. The view is along one of the pseudo-twofold axes; the other two run vertically and horizontally. Chains A and B (light and dark blue) form one dimeric subunit and chains C and D (red and orange) form the other dimer. The interfaces are shown in detail in Fig. 3[139] [link]-[140][turqarr.gif] . The four Pro residues forming a short left-handed poly-Pro helix are shown in green (see also Fig. 5[141] [link]-[142][turqarr.gif] ). For chain A the [143][alpha] -helices have been labeled from 1 to 13 and the [144][beta] -strands from A to F. This figure, as well as all molecular graphics in Figs. 3[145] [link]-[146][turqarr.gif] , 4[147] [link]-[148][turqarr.gif] and 5[149] [link]-[150][turqarr.gif] , was prepared using the program PyMol (DeLano, 2002[151] [DeLano, W. L. (2002). PyMOL. DeLano Scientific, San Carlos, CA, USA.]-[152][bluearr.gif] ). 		Figure 6.
Figure 6 Least-squares fit of the proline-rich stretch of M. tuberculosis dPGAM (residues 121-130) in blue onto a proline-rich peptide known to bind SH3 domains (taken from the structure with PDB code 1fyn ; Musacchio et al., 1994 [Musacchio, A., Saraste, M. & Wilmanns, M. (1994). Nature Struct. Biol. 1, 546-551.]-[bluearr.gif] ) in red. The two (Pro)[4] motifs overlap very well (r.m.s.d. = 0.73 Å for all atoms). This similarity supports the assumption that the four consecutive proline residues may be involved in protein-protein interactions.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 309-315) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19015259 H.Li, and G.Jogl (2009).
Structural and Biochemical Studies of TIGAR (TP53-induced Glycolysis and Apoptosis Regulator).
  J Biol Chem, 284, 1748-1754.  
16672613 H.A.Watkins, and E.N.Baker (2006).
Structural and functional analysis of Rv3214 from Mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase.
  J Bacteriol, 188, 3589-3599.
PDB code: 2a6p
16545112 K.A.Snyder, H.J.Feldman, M.Dumontier, J.J.Salama, and C.W.Hogue (2006).
Domain-based small molecule binding site annotation.
  BMC Bioinformatics, 7, 152.  
17052986 Y.Wang, L.Liu, Z.Wei, Z.Cheng, Y.Lin, and W.Gong (2006).
Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.
  J Biol Chem, 281, 39642-39648.
PDB codes: 2a9j 2f90 2h4x 2h4z 2h52 2hhj
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