Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.40 kDa 
• Atom Count: 4992 
• Residue Count: 509 
• Unique protein chains: 1

2HHJ

Human bisphosphoglycerate mutase complexed with 2,3-bisphosphoglycerate (15 days)

• DOI: 10.2210/pdb2HHJ/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-28 Released: 2006-10-24 
• Deposition Author(s): Wang, Y., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.209 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.

Wang, Y., Liu, L., Wei, Z., Cheng, Z., Lin, Y., Gong, W.

(2006) J Biol Chem 281: 39642-39648

• PubMed: 17052986 
• DOI: 10.1074/jbc.M606421200
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Bisphosphoglycerate mutase is an erythrocyte-specific enzyme catalyzing a series of intermolecular phosphoryl group transfer reactions. Its main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. In this paper, we directly observed real-time motion of the enzyme active site and the substrate during phosphoryl transfer. A series of high resolution crystal structures of human bisphosphoglycerate mutase co-crystallized with 2,3-bisphosphoglycerate, representing different time points in the phosphoryl transfer reaction, were solved. These structures not only clarify the argument concerning the substrate binding mode for this enzyme family but also depict the entire process of the key histidine phosphorylation as a "slow movie". It was observed that the enzyme conformation continuously changed during the different states of the reaction. These results provide direct evidence for an "in line" phosphoryl transfer mechanism, and the roles of some key residues in the phosphoryl transfer process are identified.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bisphosphoglycerate mutase	A, B	267	Homo sapiens	Mutation(s): 0  Gene Names: BPGM EC: 5.4.2.4 (PDB Primary Data), 5.4.2.1 (PDB Primary Data), 3.1.3.13 (PDB Primary Data), 5.4.2.11 (UniProt)
Find proteins for P07738 (Homo sapiens) Explore P07738  Go to UniProtKB:  P07738
NIH Common Fund Data Resources
PHAROS  P07738 GTEx  ENSG00000172331

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DG2	A, B	(2R)-2,3-diphosphoglyceric acid C3 H8 O10 P2 XOHUEYCVLUUEJJ-UWTATZPHSA-N
3PG	A, B	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
HAI	A	CYCLOHEXYLAMMONIUM ION C6 H14 N PAFZNILMFXTMIY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NEP	A,B	L-PEPTIDE LINKING	C6 H10 N3 O5 P		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.209 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.692	α = 90
b = 71.555	β = 90
c = 159.194	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-28 
• Released Date: 2006-10-24 
Deposition Author(s): Wang, Y., Gong, W.

Revision History 

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-07-27
  Changes: Non-polymer description