Biological Assembly 1  

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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: 251706.50 
• Atom Count: 17661 
• Residue Count: 2216 
• Unique protein chains: 1

1GZ3

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

• DOI: 10.2210/pdb1GZ3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2002-05-14 Released: 2003-05-22 
• Deposition Author(s): Yang, Z., Lanks, C.W., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.233 
• R-Value Work: 0.194 

Literature

Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme by ATP and Fumarate

Yang, Z., Lanks, C.W., Tong, L.

(2002) Structure 10: 951-960

• PubMed: 12121650 
• Primary Citation of Related Structures:  
  1GZ4


• PubMed Abstract: 
  

The regulation of human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD-ME) by ATP and fumarate may be crucial for the metabolism of glutamine for energy production in rapidly proliferating tissues and tumors. Here we report the crystal structure at 2.2 A resolution of m-NAD-ME in complex with ATP, Mn2+, tartronate, and fumarate. Our structural, kinetic, and mutagenesis studies reveal unexpectedly that ATP is an active-site inhibitor of the enzyme, despite the presence of an exo binding site. The structure also reveals the allosteric binding site for fumarate in the dimer interface. Mutations in this binding site abolished the activating effects of fumarate. Comparison to the structure in the absence of fumarate indicates a possible molecular mechanism for the allosteric function of this compound.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD-dependent malic enzyme, mitochondrial	A, B, C, D	554	Homo sapiens	Mutation(s): 2  Gene 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A, B, C, D	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MN	A, B, C, D	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
OXL	A, B, C, D	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
FUM	A, B, C, D	FUMARIC ACID C4 H4 O4 VZCYOOQTPOCHFL-OWOJBTEDSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ATP	Ki: 200000 nM BINDINGMOAD
ATP	Ki: 200000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.233 
• R-Value Work: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 71.815	α = 90.00
b = 192.653	β = 89.77
c = 110.161	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-14 
• Released Date: 2003-05-22 
• Deposition Author(s): Yang, Z., Lanks, C.W., Tong, L.

Revision History 

• Version 1.0: 2003-05-22
  Type: Initial release
• Version 1.1: 2011-11-23
  Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2018-09-19
  Type: Data collection, Database references, Source and taxonomy, Structure summary