1YNS

Crystal Structure Of Human Enolase-phosphatase E1 and its complex with a substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human e1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase

Wang, H.Pang, H.Bartlam, M.Rao, Z.

(2005) J Mol Biol 348: 917-926

  • DOI: 10.1016/j.jmb.2005.01.072
  • Primary Citation of Related Structures:  
    1ZS9, 1YNS

  • PubMed Abstract: 
  • Enolase-phosphatase E1 (MASA) is a bifunctional enzyme in the ubiquitous methionine salvage pathway that catalyzes the continuous reactions of 2,3-diketo-5-methylthio-1-phosphopentane to yield the aci-reductone metabolite using Mg2+ as cofactor. In this ...

    Enolase-phosphatase E1 (MASA) is a bifunctional enzyme in the ubiquitous methionine salvage pathway that catalyzes the continuous reactions of 2,3-diketo-5-methylthio-1-phosphopentane to yield the aci-reductone metabolite using Mg2+ as cofactor. In this study, we have determined the crystal structure of MASA and its complex with a substrate analog to 1.7A resolution by multi-wavelength anomalous diffraction and molecular replacement techniques, respectively. The structures support the proposed mechanism of phosphatase activity and further suggest the probable mechanism of enolization. We establish a model for substrate binding to describe in detail the enzymatic reaction and the formation of the transition state, which will provide insight into the reaction mechanisms of other enzymes in the same family.


    Organizational Affiliation

    Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E-1 enzyme A261Homo sapiensMutation(s): 0 
Gene Names: ENOPH1MASAMSTP145
EC: 3.1.3.77
Find proteins for Q9UHY7 (Homo sapiens)
Explore Q9UHY7 
Go to UniProtKB:  Q9UHY7
NIH Common Fund Data Resources
PHAROS:  Q9UHY7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HPO
Query on HPO

Download Ideal Coordinates CCD File 
A
2-OXOHEPTYLPHOSPHONIC ACID
C7 H15 O4 P
ACMQFLCUSWMWKH-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.017α = 90
b = 57.546β = 90
c = 87.318γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description