1PJ2

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, cofactor NADH, Mn++, and allosteric activator fumarate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Literature

Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism.

Tao, X., Yang, Z., Tong, L.

(2003) Structure 11: 1141-1150

  • DOI: 10.1016/s0969-2126(03)00168-0
  • Primary Citation of Related Structures:  
    1PJ2, 1PJ3, 1PJ4

  • PubMed Abstract: 

    • Malic enzymes catalyze the oxidative decarboxylation of L-malate to pyruvate and CO(2) with the reduction of the NAD(P)(+) cofactor in the presence of divalent cations. We report the crystal structures at up to 2.1 A resolution of human mitochondrial NAD(P)(+)-dependent malic enzyme in different pentary complexes with the natural substrate malate or pyruvate, the dinucleotide cofactor NAD(+) or NADH, the divalent cation Mn(2+), and the allosteric activator fumarate ...

    Malic enzymes catalyze the oxidative decarboxylation of L-malate to pyruvate and CO(2) with the reduction of the NAD(P)(+) cofactor in the presence of divalent cations. We report the crystal structures at up to 2.1 A resolution of human mitochondrial NAD(P)(+)-dependent malic enzyme in different pentary complexes with the natural substrate malate or pyruvate, the dinucleotide cofactor NAD(+) or NADH, the divalent cation Mn(2+), and the allosteric activator fumarate. Malate is bound deep in the active site, providing two ligands for the cation, and its C4 carboxylate group is out of plane with the C1-C2-C3 atoms, facilitating decarboxylation. The divalent cation is positioned optimally to catalyze the entire reaction. Lys183 is the general base for the oxidation step, extracting the proton from the C2 hydroxyl of malate. Tyr112-Lys183 functions as the general acid-base pair to catalyze the tautomerization of the enolpyruvate product from decarboxylation to pyruvate.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent malic enzyme, mitochondrialA, B, C, D564Homo 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
GTEx:  ENSG00000082212 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23368
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
V [auth D],
W [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N		 Ligand Interaction
LMR
Query on LMR
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]		(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N		 Ligand Interaction
FUM
Query on FUM
Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
S [auth C],
X [auth D]		FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
U [auth D]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-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: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.283α = 90
b = 117.345β = 109.79
c = 113.024γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-03-21
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary