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PDBsum entry 2qpd

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2qpd
Jmol
Contents
Protein chains
557 a.a. *
166 a.a. *
33 a.a. *
Ligands
HEM
HAS
CUA
Metals
CU1
* Residue conservation analysis
PDB id:
2qpd
Name: Oxidoreductase
Title: An unexpected outcome of surface-engineering an integral mem protein: improved crystallization of cytochrome ba3 oxidase thermus thermophilus
Structure: CytochromE C oxidase subunit 1. Chain: a. Synonym: cytochromE C oxidase polypeptide i, cytochromE C b subunit i, cytochrome cba3 subunit 1. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b. Synonym: cytochromE C oxidase polypeptide ii, cytochromE C
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: cbaa. Expressed in: thermus thermophilus hb8. Expression_system_taxid: 300852. Gene: cbab, ctac. Gene: cbad.
Resolution:
3.25Å     R-factor:   0.220     R-free:   0.307
Authors: B.Liu,V.M.Luna,Y.Chen,C.D.Stout,J.A.Fee
Key ref: B.Liu et al. (2007). An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1029-1034. PubMed id: 18084085
Date:
23-Jul-07     Release date:   11-Dec-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SJ79  (COX1_THET8) -  Cytochrome c oxidase subunit 1
Seq:
Struc:
 
Seq:
Struc:
562 a.a.
557 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SJ80  (COX2_THET8) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
168 a.a.
166 a.a.
Protein chain
Pfam   ArchSchema ?
P82543  (COXA_THET8) -  Cytochrome c oxidase polypeptide 2A
Seq:
Struc:
34 a.a.
33 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.1.9.3.1  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.64% similarity
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     oxidation-reduction process   7 terms 
  Biochemical function     electron carrier activity     7 terms  

 

 
    reference    
 
 
Acta Crystallogr Sect F Struct Biol Cryst Commun 63:1029-1034 (2007)
PubMed id: 18084085  
 
 
An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
B.Liu, V.M.Luna, Y.Chen, C.D.Stout, J.A.Fee.
 
  ABSTRACT  
 
Past work has shown that it is feasible to mutate surface residues of soluble proteins and to a lesser extent membrane proteins in order to improve their crystallization behavior. Described here is a successful application of this approach to the integral membrane protein Thermus thermophilus cytochrome ba(3) oxidase. Two mutant forms of this enzyme (I-K258R and I-K258R/II-E4Q) were created in which symmetrical crystal contacts within crystals of wild-type enzyme were modified. These mutant proteins had greatly shortened crystallization times, decreasing from approximately 30 d for the wild type to 1-3 d for the mutants, and crystallization was highly reproducible. Native-like proteins crystallize in space group P4(3)2(1)2, whereas the mutant proteins crystallize in space group P4(1)2(1)2 with a different packing arrangement. Crystals of the P4(3)2(1)2 form occasionally diffracted to 2.4-2.3 A resolution following controlled dehydration, while those of the P4(1)2(1)2 form routinely diffracted to between 3.0 and 2.6 A for crystals that had been cryoprotected but not dehydrated.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19342785 T.Shimamura, Y.Nitanai, T.Uchiyama, and H.Matsuzawa (2009).
Improvement of crystal quality by surface mutations of beta-lactamase Toho-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 379-382.
PDB code: 2zq8
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