2HHJ

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

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 

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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

  • DOI: 10.1074/jbc.M606421200
  • Primary Citation of Related Structures:  
    2A9J, 2F90, 2H4X, 2H4Z, 2HHJ

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bisphosphoglycerate mutaseA, B267Homo sapiensMutation(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)
UniProt & NIH Common Fund Data Resources
Find proteins for P07738 (Homo sapiens)
Explore P07738 
Go to UniProtKB:  P07738
PHAROS:  P07738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07738
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DG2
Query on DG2
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		(2R)-2,3-diphosphoglyceric acid
C3 H8 O10 P2
XOHUEYCVLUUEJJ-UWTATZPHSA-N		 Ligand Interaction
3PG
Query on 3PG
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N		 Ligand Interaction
HAI
Query on HAI
Download Ideal Coordinates CCD File 
C [auth A]CYCLOHEXYLAMMONIUM ION
C6 H14 N
PAFZNILMFXTMIY-UHFFFAOYSA-O		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP		A, B L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
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 = 48.692α = 90
b = 71.555β = 90
c = 159.194γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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