1EFL

HUMAN MALIC ENZYME IN A QUATERNARY COMPLEX WITH NAD, MG, AND TARTRONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.206 

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.Mol.Biol. 7: 251-257

  • DOI: 10.1038/73378
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALIC ENZYME
A, B, C, D
584Homo sapiensGene Names: ME2
EC: 1.1.1.38
Find proteins for P23368 (Homo sapiens)
Go to Gene View: ME2
Go to UniProtKB:  P23368
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTN
Query on TTN

Download SDF File 
Download CCD File 
A, B, C, D
TARTRONATE
C3 H2 O5
ROBFUDYVXSDBQM-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 228.800α = 90.00
b = 117.000β = 109.20
c = 114.300γ = 90.00
Software Package:
Software NamePurpose
GLRFphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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