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PDBsum entry 4by3

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
4by3
Jmol PyMol
Contents
Protein chain
362 a.a.
Ligands
FMT ×4
Metals
_ZN ×4
Waters ×397
PDB id:
4by3
Name: Hydrolase
Title: Crystal structure of the dihydroorotase domain of human cad in apo-form obtained recombinantly from e. Coli.
Structure: Dihydroorotase. Chain: a. Fragment: residues 1456-1846. Synonym: cad protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta plyss.
Resolution:
1.73Å     R-factor:   0.126     R-free:   0.136
Authors: S.Ramon-Maiques,N.Lallous,A.Grande-Garcia
Key ref: A.Grande-García et al. (2014). Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD. Structure, 22, 185-198. PubMed id: 24332717 DOI: 10.1016/j.str.2013.10.016
Date:
17-Jul-13     Release date:   28-May-14    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
-  (POLG_HAVHM) - 
Protein chain
Pfam   ArchSchema ?
P27708  (PYR1_HUMAN) -  CAD protein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2225 a.a.
362 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.2.1.3.2  - Aspartate carbamoyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pyrimidine Biosynthesis
      Reaction: Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
Carbamoyl phosphate
+ L-aspartate
= phosphate
+ N-carbamoyl-L-aspartate
   Enzyme class 3: E.C.3.5.2.3  - Dihydroorotase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
(S)-dihydroorotate
+ H(2)O
= N-carbamoyl-L-aspartate
   Enzyme class 4: E.C.6.3.5.5  - Carbamoyl-phosphate synthase (glutamine-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: 2 ATP + L-glutamine + HCO3- + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate
2 × ATP
+ L-glutamine
+
HCO(3)(-)
Bound ligand (Het Group name = FMT)
matches with 75.00% similarity
+ H(2)O
= 2 × ADP
+ phosphate
+ L-glutamate
+ carbamoyl phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2013.10.016 Structure 22:185-198 (2014)
PubMed id: 24332717  
 
 
Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD.
A.Grande-García, N.Lallous, C.Díaz-Tejada, S.Ramón-Maiques.
 
  ABSTRACT  
 
Upregulation of CAD, the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals, is essential for cell proliferation. Deciphering the architecture and functioning of CAD is of interest for its potential usage as an antitumoral target. However, there is no detailed structural information about CAD other than that it self-assembles into hexamers of ∼1.5 MDa. Here we report the crystal structure and functional characterization of the dihydroorotase domain of human CAD. Contradicting all assumptions, the structure reveals an active site enclosed by a flexible loop with two Zn(2+) ions bridged by a carboxylated lysine and a third Zn coordinating a rare histidinate ion. Site-directed mutagenesis and functional assays prove the involvement of the Zn and flexible loop in catalysis. Comparison with homologous bacterial enzymes supports a reclassification of the DHOase family and provides strong evidence against current models of the architecture of CAD.
 

 

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