1EFK

STRUCTURE OF HUMAN MALIC ENZYME IN COMPLEX WITH KETOMALONATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of a closed form of human malic enzyme and implications for catalytic mechanism.

Yang, Z., Floyd, D.L., Loeber, G., Tong, L.

(2000) Nat Struct Biol 7: 251-257

  • DOI: 10.1038/73378
  • Primary Citation of Related Structures:  
    1EFL, 1EFK, 1DO8

  • PubMed Abstract: 

    • Malic enzymes are widely distributed in nature and have many biological functions. The crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a quaternary complex with NAD+, Mn++ and oxalate has been determined at 2.2 A resolution. The structures of the quaternary complex with NAD+, Mg++, tartronate or ketomalonate have been determined at 2 ...

    Malic enzymes are widely distributed in nature and have many biological functions. The crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a quaternary complex with NAD+, Mn++ and oxalate has been determined at 2.2 A resolution. The structures of the quaternary complex with NAD+, Mg++, tartronate or ketomalonate have been determined at 2.6 A resolution. The structures show the enzyme in a closed form in these complexes and reveal the binding modes of the cation and the inhibitors. The divalent cation is coordinated in an octahedral fashion by six ligating oxygens, two from the substrate/inhibitor, three from Glu 255, Asp 256 and Asp 279 of the enzyme, and one from a water molecule. The structural information has significant implications for the catalytic mechanism of malic enzymes and identifies Tyr 112 and Lys 183 as possible catalytic residues. Changes in tetramer organization of the enzyme are also observed in these complexes, which might be relevant for its cooperative behavior and allosteric control.

    Organizational Affiliation: 

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALIC ENZYME A, B, C, D584Homo sapiensMutation(s): 14 
Gene Names: ME2
EC: 1.1.1.39 (PDB Primary Data), 1.1.1.38 (UniProt)
Find proteins for P23368 (Homo sapiens)
Explore P23368 
Go to UniProtKB:  P23368
NIH Common Fund Data Resources
PHAROS:  P23368
GTEx:  ENSG00000082212
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 229.6α = 90
b = 118.6β = 109.6
c = 113.1γ = 90
Software Package:
Software NamePurpose
GLRFphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance