spacer
spacer

PDBsum entry 3ehb

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase/immune system PDB id
3ehb
Jmol
Contents
Protein chains
530 a.a. *
253 a.a. *
119 a.a. *
109 a.a. *
Ligands
HEA ×2
LDA ×9
LMT ×12
PER
Metals
_CU ×3
_MG
_CA
Waters ×379
* Residue conservation analysis
PDB id:
3ehb
Name: Oxidoreductase/immune system
Title: A d-pathway mutation decouples the paracoccus denitrificans cytochromE C oxidase by altering the side chain orientation of a distant, conserved glutamate
Structure: CytochromE C oxidase subunit 1-beta. Chain: a. Fragment: unp residues 17-545. Synonym: cytochromE C oxidase polypeptide i-beta, cytochrome aa3 subunit 1-beta. Engineered: yes. Mutation: yes. CytochromE C oxidase subunit 2. Chain: b.
Source: Paracoccus denitrificans. Organism_taxid: 266. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. Mouse. Organism_taxid: 10090. Expression_system_taxid: 562
Resolution:
2.32Å     R-factor:   0.206     R-free:   0.242
Authors: J.Koepke,H.Mueller,G.Peng
Key ref:
K.L.Dürr et al. (2008). A D-pathway mutation decouples the paracoccusdenitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. J Mol Biol, 384, 865-877. PubMed id: 18930738 DOI: 10.1016/j.jmb.2008.09.074
Date:
12-Sep-08     Release date:   30-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P98002  (COX1B_PARDE) -  Cytochrome c oxidase subunit 1-beta
Seq:
Struc:
 
Seq:
Struc:
558 a.a.
530 a.a.*
Protein chain
Pfam   ArchSchema ?
P08306  (COX2_PARDE) -  Cytochrome c oxidase subunit 2
Seq:
Struc:
298 a.a.
253 a.a.
Protein chain
Pfam   ArchSchema ?
P18525  (HVM54_MOUSE) -  Ig heavy chain V region 5-84
Seq:
Struc:
117 a.a.
119 a.a.*
Protein chain
Pfam   ArchSchema ?
P01636  (KV5A4_MOUSE) -  Ig kappa chain V-V region MOPC 149
Seq:
Struc:
108 a.a.
109 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 21 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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 = HEA)
matches with 50.00% similarity
+
O(2)
Bound ligand (Het Group name = PER)
corresponds exactly
+ 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   8 terms 
  Biochemical function     electron carrier activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2008.09.074 J Mol Biol 384:865-877 (2008)
PubMed id: 18930738  
 
 
A D-pathway mutation decouples the paracoccusdenitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate.
K.L.Dürr, J.Koepke, P.Hellwig, H.Müller, H.Angerer, G.Peng, E.Olkhova, O.M.Richter, B.Ludwig, H.Michel.
 
  ABSTRACT  
 
Asparagine 131, located near the cytoplasmic entrance of the D-pathway in subunit I of the Paracoccus denitrificans aa(3) cytochrome c oxidase, is a residue crucial for proton pumping. When replaced by an aspartate, the mutant enzyme is completely decoupled: while retaining full cytochrome c oxidation activity, it does not pump protons. The same phenotype is observed for two other substitutions at this position (N131E and N131C), whereas a conservative replacement by glutamine affects both activities of the enzyme. The N131D variant oxidase was crystallized and its structure was solved to 2.32-A resolution, revealing no significant overall change in the protein structure when compared with the wild type (WT), except for an alternative orientation of the E278 side chain in addition to its WT conformation. Moreover, remarkable differences in the crystallographically resolved chain of water molecules in the D-pathway are found for the variant: four water molecules that are observed in the water chain between N131 and E278 in the WT structure are not visible in the variant, indicating a higher mobility of these water molecules. Electrochemically induced Fourier transform infrared difference spectra of decoupled mutants confirm that the protonation state of E278 is unaltered by these mutations but indicate a distinct perturbation in the hydrogen-bonding environment of this residue. Furthermore, they suggest that the carboxylate side chain of the N131D mutant is deprotonated. These findings are discussed in terms of their mechanistic implications for proton routing through the D-pathway of cytochrome c oxidase.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structures of subunits I and II of the four-subunit complex of the aa[3] COX from P. denitrificans (Protein Data Bank code 1AR1) illustrating the two proton-conducting pathways of the enzyme: D-pathway (red) and K-pathway (green). A putative proton exit pathway is also indicated (black arrow). Functionally important amino acid side chains in the pathways (including N131) are represented as sticks.
Figure 3.
Fig. 3. (A) Oxidized-minus-reduced FTIR difference spectra of WT and N131D, N131C, and N199D mutant COXs from P. denitrificans for a potential step from − 0.5 to 0.5 V versus Ag/AgCl (corresponding to a potential step from − 0.292 to 0.708 V SHE′). (B) Oxidized-minus-reduced FTIR difference spectra of WT (dashed dotted line), N131D (continuous line), and N131C (dashed line) COXs from P. denitrificans for a potential step from − 0.5 to 0.5 V versus Ag/AgCl (corresponding to a potential step from − 0.292 to 0.708 V SHE′). (C) Oxidized-minus-reduced FTIR difference spectra of WT (dashed-dotted line) and N131C variant (continuous line) COXs from P. denitrificans, with samples equilibrated at pH 9.2, for a potential step from − 0.5 to 0.5 V versus Ag/AgCl (corresponding to a potential step from − 0.292 to 0.708 V SHE′).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 865-877) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205904 J.Liu, L.Qin, and S.Ferguson-Miller (2011).
Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
  Proc Natl Acad Sci U S A, 108, 1284-1289.
PDB codes: 3om3 3oma 3omi 3omn
21545285 S.Yoshikawa, K.Muramoto, and K.Shinzawa-Itoh (2011).
Proton-pumping mechanism of cytochrome C oxidase.
  Annu Rev Biophys, 40, 205-223.  
20192226 S.A.Siletsky, J.Zhu, R.B.Gennis, and A.A.Konstantinov (2010).
Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel.
  Biochemistry, 49, 3060-3073.  
19303362 B.Kadenbach, R.Ramzan, and S.Vogt (2009).
Degenerative diseases, oxidative stress and cytochrome c oxidase function.
  Trends Mol Med, 15, 139-147.  
19219012 E.Schleiff, and R.Tampé (2009).
Membrane proteins take center stage in Frankfurt.
  Nat Chem Biol, 5, 135-139.  
19805275 H.Y.Chang, J.Hemp, Y.Chen, J.A.Fee, and R.B.Gennis (2009).
The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping.
  Proc Natl Acad Sci U S A, 106, 16169-16173.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.