Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 36247.57 
• Atom Count: 2536 
• Residue Count: 321 
• Unique protein chains: 1

1EP9

HUMAN ORNITHINE TRANSCARBAMYLASE: CRYSTALLOGRAPHIC INSIGHTS INTO SUBSTRATE RECOGNITION AND CONFORMATIONAL CHANGE

• DOI: 10.2210/pdb1EP9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2000-03-28 Released: 2001-04-04 
• Deposition Author(s): Shi, D., Morizono, H., Yu, X., Allewell, N.M., Tuchman, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.223 
• R-Value Work: 0.184 

Literature

Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes.

Shi, D., Morizono, H., Yu, X., Tong, L., Allewell, N.M., Tuchman, M.

(2001) Biochem.J. 354: 501-509

• PubMed: 11237854 
• Primary Citation of Related Structures:  
  1FVO


• PubMed Abstract: 
  

Two crystal structures of human ornithine transcarbamylase (OTCase) complexed with the substrate carbamoyl phosphate (CP) have been solved. One structure, whose crystals were prepared by substituting N-phosphonacetyl-L-ornithine (PALO) liganded crystals with CP, has been refined at 2.4 A (1 A=0.1 nm) resolution to a crystallographic R factor of 18.4%. The second structure, whose crystals were prepared by co-crystallization with CP, has been refined at 2.6 A resolution to a crystallographic R factor of 20.2%. These structures provide important new insights into substrate recognition and ligand-induced conformational changes. Comparison of these structures with the structures of OTCase complexed with the bisubstrate analogue PALO or CP and L-norvaline reveals that binding of the first substrate, CP, induces a global conformational change involving relative domain movement, whereas the binding of the second substrate brings the flexible SMG loop, which is equivalent to the 240s loop in aspartate transcarbamylase, into the active site. The model reveals structural features that define the substrate specificity of the enzyme and that regulate the order of binding and release of products.

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Organizational Affiliation: 

Children's National Medical Center, 111 Michigan Avenue, Washington, DC 20010, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ORNITHINE TRANSCARBAMYLASE	A	321	Homo sapiens	Mutation(s): 0  Gene Names: OTC EC: 2.1.3.3
Find proteins for P00480 (Homo sapiens) Go to Gene View: OTC Go to UniProtKB:  P00480

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CP	A	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H4 N O5 P FFQKYPRQEYGKAF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.223 
• R-Value Work: 0.184 
• Space Group: P 2₁ 3

Unit Cell:

Length (Å)	Angle (°)
a = 125.600	α = 90.00
b = 125.600	β = 90.00
c = 125.600	γ = 90.00

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-PLOR	refinement
X-GEN	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-28 
• Released Date: 2001-04-04 
• Deposition Author(s): Shi, D., Morizono, H., Yu, X., Allewell, N.M., Tuchman, M.

Revision History 

• Version 1.0: 2001-04-04
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description