6HG1

Hybrid dihydroorotase domain of human CAD with E. coli flexible loop in apo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD.

Del Cano-Ochoa, F.Grande-Garcia, A.Reverte-Lopez, M.D'Abramo, M.Ramon-Maiques, S.

(2018) J Biol Chem 293: 18903-18913

  • DOI: https://doi.org/10.1074/jbc.RA118.005494
  • Primary Citation of Related Structures:  
    6HFD, 6HFE, 6HFF, 6HFH, 6HFI, 6HFJ, 6HFK, 6HFL, 6HFN, 6HFP, 6HFQ, 6HFR, 6HFS, 6HFU, 6HG1, 6HG2, 6HG3

  • PubMed Abstract: 

    The dihydroorotase (DHOase) domain of the multifunctional protein carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) catalyzes the third step in the de novo biosynthesis of pyrimidine nucleotides in animals. The crystal structure of the DHOase domain of human CAD (huDHOase) revealed that, despite evolutionary divergence, its active site components are highly conserved with those in bacterial DHOases, encoded as monofunctional enzymes. An important element for catalysis, conserved from Escherichia coli to humans, is a flexible loop that closes as a lid over the active site. Here, we combined mutagenic, structural, biochemical, and molecular dynamics analyses to characterize the function of the flexible loop in the activity of CAD's DHOase domain. A huDHOase chimera bearing the E. coli DHOase flexible loop was inactive, suggesting the presence of distinctive elements in the flexible loop of huDHOase that cannot be replaced by the bacterial sequence. We pinpointed Phe-1563, a residue absolutely conserved at the tip of the flexible loop in CAD's DHOase domain, as a critical element for the conformational equilibrium between the two catalytic states of the protein. Substitutions of Phe-1563 with Ala, Leu, or Thr prevented the closure of the flexible loop and inactivated the protein, whereas substitution with Tyr enhanced the interactions of the loop in the closed position and reduced fluctuations and the reaction rate. Our results confirm the importance of the flexible loop in CAD's DHOase domain and explain the key role of Phe-1563 in configuring the active site and in promoting substrate strain and catalysis.


  • Organizational Affiliation

    the Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CAD protein,Dihydroorotase,CAD protein371Homo sapiensEscherichia coli K-12Mutation(s): 0 
Gene Names: CADpyrCb1062JW1049
EC: 6.3.5.5 (PDB Primary Data), 2.1.3.2 (PDB Primary Data), 3.5.2.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P27708 (Homo sapiens)
Explore P27708 
Go to UniProtKB:  P27708
GTEx:  ENSG00000084774 
Find proteins for P05020 (Escherichia coli (strain K12))
Explore P05020 
Go to UniProtKB:  P05020
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP27708P05020
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.049α = 90
b = 160.591β = 90
c = 58.984γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-80570-R

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description