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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALIC ENZYMEA, B, C, D584Homo sapiensMutation(s): 14 
Gene Names: ME2
EC: 1.1.1.39 (PDB Primary Data), 1.1.1.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23368 (Homo sapiens)
Explore P23368 
Go to UniProtKB:  P23368
PHAROS:  P23368
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MAK
Query on MAK

Download Ideal Coordinates CCD File 
H [auth A], L [auth B], P [auth C], T [auth D]ALPHA-KETOMALONIC ACID
C3 H2 O5
XEEVLJKYYUVTRC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], M [auth C], Q [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
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

View Full Validation Report



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