Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 262.12 kDa 
• Atom Count: 18640 
• Modelled Residue Count: 2212 
• Deposited Residue Count: 2256 
• Unique protein chains: 1

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

• DOI: 10.2210/pdb1PJ2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-30 Released: 2003-11-11 
• Deposition Author(s): Tao, X., Yang, Z., Tong, L.

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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 

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

• PubMed: 12962632 
• DOI: 10.1016/s0969-2126(03)00168-0
• Primary Citation of Related Structures:  
  1PJ2, 1PJ4, 1PJ3


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent malic enzyme, mitochondrial	A, B, C, D	564	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	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
LMR	E [auth A], J [auth B], O [auth C], T [auth D]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N
FUM	I [auth A], N [auth B], S [auth C], X [auth D]	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N
MN	F [auth A], K [auth B], P [auth C], U [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 227.283	α = 90
b = 117.345	β = 109.79
c = 113.024	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-30 
• Released Date: 2003-11-11 
Deposition Author(s): Tao, X., Yang, Z., Tong, L.

Revision History  

• 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