1EP9

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: 10.1042/0264-6021:3540501
  • Primary Citation of Related Structures:  
    1EP9, 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 ...

    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.

    Organizational Affiliation: 

    Children's National Medical Center, 111 Michigan Avenue, Washington, DC 20010, USA. dshi@childrens-research.org



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORNITHINE TRANSCARBAMYLASEA321Homo sapiensMutation(s): 0 
Gene Names: OTC
EC: 2.1.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00480 (Homo sapiens)
Explore P00480 
Go to UniProtKB:  P00480
PHAROS:  P00480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00480
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CP
Query on CP
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
C H4 N O5 P
FFQKYPRQEYGKAF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.6α = 90
b = 125.6β = 90
c = 125.6γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
X-GENdata reduction
X-GENdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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