1GZ3 | pdb_00001gz3

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

PDB DOI: https://doi.org/10.2210/pdb1GZ3/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.233 (Depositor)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00788-8
Primary Citation Related Structures:
1GZ3, 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 251.71 kDa
Atom Count: 18,818
Modeled Residue Count: 2,216
Deposited Residue Count: 2,216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent malic enzyme, mitochondrial	A, B, C, D	554	Homo sapiens	Mutation(s): 2 Gene Names: ME2 EC: 1.1.1.38
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23368
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], I [auth B], M [auth C], Q [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
FUM Query on FUM Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], P [auth C], T [auth D]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
OXL Query on OXL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], N [auth C], R [auth D]	OXALATE ION C₂ O₄ MUBZPKHOEPUJKR-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C], S [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.233 (Depositor)
R-Value Work: 0.194 (Depositor)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.815	α = 90
b = 192.653	β = 89.77
c = 110.161	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-05-22

Deposition Author(s):

Yang, Z.

Lanks, C.W.

Tong, L.

Revision History (Full details and data files)

Version 1.0: 2003-05-22
Type: Initial release
Version 1.1: 2011-11-23
Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
Version 1.2: 2018-09-19
Changes: Data collection, Database references, Source and taxonomy, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-05-01
Changes: Refinement description