Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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,PQS (software)

Macromolecule Content

• Total Structure Weight: 138679.78 
• Atom Count: 9620 
• Residue Count: 1210 
• Unique protein chains: 1

1O0S

Crystal Structure of Ascaris suum Malic Enzyme Complexed with NADH

• DOI: 10.2210/pdb1O0S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ascaris suum


• Deposited: 2003-02-24 Released: 2003-07-22 
• Deposition Author(s): Rao, G.S., Coleman, D.E., Karsten, W.E., Cook, P.F., Harris, B.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.264 
• R-Value Work: 0.221 

Literature

Crystallographic studies on Ascaris suum NAD-malic enzyme bound to reduced cofactor and identification of an effector site.

Rao, G.S., Coleman, D.E., Karsten, W.E., Cook, P.F., Harris, B.G.

(2003) J.Biol.Chem. 278: 38051-38058

• PubMed: 12853453 
• DOI: 10.1074/jbc.M305145200


• PubMed Abstract: 
  

The crystal structure of the mitochondrial NAD-malic enzyme from Ascaris suum, in a quaternary complex with NADH, tartronate, and magnesium has been determined to 2.0-A resolution. The structure closely resembles the previously determined structure of the same enzyme in binary complex with NAD. However, a significant difference is observed within the coenzyme-binding pocket of the active site with the nicotinamide ring of NADH molecule rotating by 198 degrees over the C-1-N-1 bond into the active site without causing significant movement of the other catalytic residues. The implications of this conformational change in the nicotinamide ring to the catalytic mechanism are discussed. The structure also reveals a binding pocket for the divalent metal ion in the active site and a binding site for tartronate located in a highly positively charged environment within the subunit interface that is distinct from the active site. The tartronate binding site, presumably an allosteric site for the activator fumarate, shows striking similarities and differences with the activator site of the human NAD-malic enzyme that has been reported recently. Thus, the structure provides additional insights into the catalytic as well as the allosteric mechanisms of the enzyme.

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Related Citations: 

• Crystal Structure of the Malic Enzyme from Ascaris suum Complexed with Nicotinamide Adenine Dinucleotide at 2.3 A Resolution
  Coleman, D.E.,Rao, G.S.J.,Goldsmith, E.J.,Cook, P.F.,Harris, B.G.
  (2002) Biochemistry 41: 6928




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Organizational Affiliation: 

Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD-dependent malic enzyme	A, B	605	Ascaris suum	Mutation(s): 0  EC: 1.1.1.38
Find proteins for P27443 (Ascaris suum) Go to UniProtKB:  P27443

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TTN	A, B	TARTRONATE C3 H2 O5 ROBFUDYVXSDBQM-UHFFFAOYSA-L
NAI	A, B	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE NADH C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.264 
• R-Value Work: 0.221 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 130.947	α = 90.00
b = 130.947	β = 90.00
c = 149.128	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-24 
• Released Date: 2003-07-22 
• Deposition Author(s): Rao, G.S., Coleman, D.E., Karsten, W.E., Cook, P.F., Harris, B.G.

Revision History 

• Version 1.0: 2003-07-22
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Type: Advisory, Refinement description