PDBsum entry: 1t8p

Isomerase

PDB id: 1t8p

Contents

Protein chains

249 a.a. *

Waters ×232

* Residue conservation analysis

PDB id:

1t8p

Name:

Isomerase

Title:

Crystal structure of human erythrocyte 2,3- bisphosphoglycerate mutase

Structure:

Bisphosphoglycerate mutase. Chain: a, b. Synonym: 2,3-bisphosphoglycerate mutase, erythrocyte, 2,3- bisphosphoglycerate synthase, bpgm. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.200 R-free: 0.266

Authors:

Y.Wang,Z.Wei,Q.Bian,Z.Cheng,M.Wan,L.Liu,W.Gong

Key ref:

Y.Wang et al. (2004). Crystal structure of human bisphosphoglycerate mutase. J Biol Chem, 279, 39132-39138. PubMed id: 15258155 DOI: 10.1074/jbc.M405982200

Date:

13-May-04 Release date: 10-Aug-04

Protein chains

P07738  (PMGE_HUMAN) -  Bisphosphoglycerate mutase

Seq: 259 a.a.

Struc: 249 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.1.3.13 - Bisphosphoglycerate phosphatase.
• Reaction: 2,3-bisphospho-D-glycerate + H₂O = 3-phospho-D-glycerate + phosphate
• Enzyme class 3: E.C.5.4.2.1 - Phosphoglycerate mutase.
• Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
• Enzyme class 4: E.C.5.4.2.4 - Bisphosphoglycerate mutase.
• Reaction: 3-phospho-D-glyceroyl phosphate = 2,3-bisphospho-D-glycerate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (5 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1074/jbc.M405982200

J Biol Chem 279:39132-39138 (2004)

PubMed id: 15258155

Crystal structure of human bisphosphoglycerate mutase.

Y.Wang, Z.Wei, Q.Bian, Z.Cheng, M.Wan, L.Liu, W.Gong.

ABSTRACT

Bisphosphoglycerate mutase is a trifunctional enzyme of which the main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. The gene coding for bisphosphoglycerate mutase from the human cDNA library was cloned and expressed in Escherichia coli. The protein crystals were obtained and diffract to 2.5 A and produced the first crystal structure of bisphosphoglycerate mutase. The model was refined to a crystallographic R-factor of 0.200 and R(free) of 0.266 with excellent stereochemistry. The enzyme remains a dimer in the crystal. The overall structure of the enzyme resembles that of the cofactor-dependent phosphoglycerate mutase except the regions of 13-21, 98-117, 127-151, and the C-terminal tail. The conformational changes in the backbone and the side chains of some residues reveal the structural basis for the different activities between phosphoglycerate mutase and bisphosphoglycerate mutase. The bisphosphoglycerate mutase-specific residue Gly-14 may cause the most important conformational changes, which makes the side chain of Glu-13 orient toward the active site. The positions of Glu-13 and Phe-22 prevent 2,3-bisphosphoglycerate from binding in the way proposed previously. In addition, the side chain of Glu-13 would affect the Glu-89 protonation ability responsible for the low mutase activity. Other structural variations, which could be connected with functional differences, are also discussed.

Selected figure(s)

Figure 3.
FIG. 3. The dimer of hBPGM viewed along the non-crystallographic 2-fold axis.

Figure 6.
FIG. 6. The electron density map (2F[o] - F[c], 1.0 ) of Ser-24. The hydrogen bond between Ser-24 and Arg-90 is labeled. The and angles of this residue are 53.5° and -125.1°, respectively. These two angles in the equivalent residue Gly in E. coli dPGM are 61.4° and -130.8°, and in S. cerevisiae dPGM are 67.6° and -124.9°, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 39132-39138) copyright 2004.

Figures were selected by an automated process.