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PDBsum entry 2cua

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protein ligands metals Protein-protein interface(s) links
Electron transport PDB id
2cua
Jmol
Contents
Protein chains
122 a.a. *
132 a.a. *
Ligands
CUA ×2
Metals
_ZN ×2
Waters ×186
* Residue conservation analysis
PDB id:
2cua
Name: Electron transport
Title: The cua domain of cytochrome ba3 from thermus thermophilus
Structure: Protein (cua). Chain: a, b. Fragment: soluble cua-containing domain. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
1.60Å     R-factor:   0.226     R-free:   0.296
Authors: P.A.Williams,N.J.Blackburn,D.Sanders,H.Bellamy,E.A.Stura, J.A.Fee,D.E.Mcree
Key ref:
P.A.Williams et al. (1999). The CuA domain of Thermus thermophilus ba3-type cytochrome c oxidase at 1.6 A resolution. Nat Struct Biol, 6, 509-516. PubMed id: 10360350 DOI: 10.1038/9274
Date:
18-Feb-99     Release date:   28-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P98052  (COX2_THETH) -  Cytochrome c oxidase subunit 2 (Fragment)
Seq:
Struc:
135 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P98052  (COX2_THETH) -  Cytochrome c oxidase subunit 2 (Fragment)
Seq:
Struc:
135 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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
+ 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   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1038/9274 Nat Struct Biol 6:509-516 (1999)
PubMed id: 10360350  
 
 
The CuA domain of Thermus thermophilus ba3-type cytochrome c oxidase at 1.6 A resolution.
P.A.Williams, N.J.Blackburn, D.Sanders, H.Bellamy, E.A.Stura, J.A.Fee, D.E.McRee.
 
  ABSTRACT  
 
The structure of the CuA-containing, extracellular domain of Thermus thermophilus ba3-type cytochrome c oxidase has been determined to 1.6 A resolution using multiple X-ray wavelength anomalous dispersion (MAD). The Cu2S2 cluster forms a planar rhombus with a copper-copper distance of 2.51 +/- 0.03 A. X-ray absorption fine-structure (EXAFS) studies show that this distance is unchanged by crystallization. The CuA center is asymmetrical; one copper is tetrahedrally coordinated to two bridging cysteine thiolates, one histidine nitrogen and one methionine sulfur, while the other is trigonally coordinated by the two cysteine thiolates and a histidine nitrogen. Combined sequence-structure alignment of amino acid sequences reveals conserved interactions between cytochrome c oxidase subunits I and II.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. a, Stereo ribbon diagram of Thermus ba[3]-Cu[ A], with the position of every 10th amino acid labeled. The eight -strands that make up the -sandwich are colored indicating the sheet to which they belong. The protein ligands to the Cu[A] center (the two blue spheres) are shown as ball-and-stick, and the copper atoms are depicted as spheres. The figure was made using BOBSCRIPT, and rendered using Raster3D. b, Topology diagram of Thermus ba[3]-Cu[ A] with the -strands labeled according to the cupredoxin convention. c, Sequence alignment of Thermus ba[3]-Cu[A] protein with subunit II of cytochrome c oxidase from bovine heart mitochondria and Paracoccus denitrificans, along with the sequence of the engineered CyoA protein from Escherichia coli quinol oxidase. Also included is the sequence of a representative type I copper protein, pseudoazurin from Alcaligenes faecalis. The alignment was based on both structure and sequence. The sequence alignment was created using CKWHENCE, written by C.M. Bruns (http://www.scripps.edu/~bruns/ckwhence.html); the figure created using ESPcript (P. Gouet et al., http://www.ipbs.fr/ESPript). The secondary-structure assignment of cytochrome c oxidase is shown above the alignment, along with the nomenclature for the -strands of the cupredoxin fold. The insert region, which separates strands 2A and 2B, is shown in blue, and the linker region is shown in green. The copper ligands are shown in bold red.
Figure 2.
Figure 2. a, A schematic diagram of the geometry of the Thermus ba[3]-Cu[A] center. The distances shown are the averaged values for the two molecules. His 157 and Met 160 are below the Cu[2]S[2] plane (the Cu1−Cu2−ND1(His 157) angle is 157.8°, while the SG(Cys 149)−Cu1-SD(Met 160) angle is 110.2°); His 114 and Gln 151 are above the plane (Cu2-Cu1-ND1(His 114) 139.6°, SG(Cys 153)-Cu2-O(Gln 151) 103.1°). b,c, Stereo pictures of the Cu[A] center of Thermus ba[3]-Cu[ A]. The SigmaA-weighted electron density in blue is contoured at 1.0 (where represents the r.m.s. electron density for the unit cell) and at 10 in red. The elongation of the density around the center is in the direction of the a axis in both copies of the molecule and appears to be due to a relatively higher disorder in the crystal packing. The figure was prepared using BOBSCRIPT, and rendered using Raster3D.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 509-516) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20169379 M.G.Savelieff, and Y.Lu (2010).
Cu(A) centers and their biosynthetic models in azurin.
  J Biol Inorg Chem, 15, 461-483.  
19146411 L.A.Abriata, G.N.Ledesma, R.Pierattelli, and A.J.Vila (2009).
Electronic structure of the ground and excited states of the Cu(A) site by NMR spectroscopy.
  J Am Chem Soc, 131, 1939-1946.  
18766386 Y.El Khoury, and P.Hellwig (2009).
Infrared spectroscopic characterization of copper-polyhistidine from 1,800 to 50 cm(-1): model systems for copper coordination.
  J Biol Inorg Chem, 14, 23-34.  
18253516 N.A.Sieracki, H.J.Hwang, M.K.Lee, D.K.Garner, and Y.Lu (2008).
A temperature independent pH (TIP) buffer for biomedical biophysical applications at low temperatures.
  Chem Commun (Camb), (), 823-825.  
17681231 S.D.Katewa, and J.W.Ballard (2007).
Sympatric Drosophila simulans flies with distinct mtDNA show age related differences in mitochondrial metabolism.
  Insect Biochem Mol Biol, 37, 923-932.  
16554303 L.Muresanu, P.Pristovsek, F.Löhr, O.Maneg, M.D.Mukrasch, H.Rüterjans, B.Ludwig, and C.Lücke (2006).
The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase. A combined NMR and computational approach.
  J Biol Chem, 281, 14503-14513.
PDB code: 2fwl
15632131 T.Iwasaki, A.Kounosu, Y.Tao, Z.Li, J.E.Shokes, N.J.Cosper, T.Imai, A.Urushiyama, and R.A.Scott (2005).
Rational design of a mononuclear metal site into the archaeal Rieske-type protein scaffold.
  J Biol Chem, 280, 9129-9134.  
15139821 D.Goldfarb, and D.Arieli (2004).
Spin distribution and the location of protons in paramagnetic proteins.
  Annu Rev Biophys Biomol Struct, 33, 441-468.  
15326290 H.J.Hwang, and Y.Lu (2004).
pH-dependent transition between delocalized and trapped valence states of a CuA center and its possible role in proton-coupled electron transfer.
  Proc Natl Acad Sci U S A, 101, 12842-12847.  
15211513 L.L.Videau, W.B.Arendall, and J.S.Richardson (2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.
  Proteins, 56, 298-309.  
11964261 D.Lukoyanov, S.M.Berry, Y.Lu, W.E.Antholine, and C.P.Scholes (2002).
Role of the coordinating histidine in altering the mixed valency of Cu(A): an electron nuclear double resonance-electron paramagnetic resonance investigation.
  Biophys J, 82, 2758-2766.  
11841221 Y.Zhen, B.Schmidt, U.G.Kang, W.Antholine, and S.Ferguson-Miller (2002).
Mutants of the CuA site in cytochrome c oxidase of Rhodobacter sphaeroides: I. Spectral and functional properties.
  Biochemistry, 41, 2288-2297.  
11340051 B.E.Schultz, and S.I.Chan (2001).
Structures and proton-pumping strategies of mitochondrial respiratory enzymes.
  Annu Rev Biophys Biomol Struct, 30, 23-65.  
11282344 I.Moura, and J.J.Moura (2001).
Structural aspects of denitrifying enzymes.
  Curr Opin Chem Biol, 5, 168-175.  
11133964 M.Santana, M.M.Pereira, N.P.Elias, C.M.Soares, and M.Teixeira (2001).
Gene cluster of Rhodothermus marinus high-potential iron-sulfur Protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.
  J Bacteriol, 183, 687-699.  
10691974 J.M.Charnock, A.Dreusch, H.Körner, F.Neese, J.Nelson, A.Kannt, H.Michel, C.D.Garner, P.M.Kroneck, and W.G.Zumft (2000).
Structural investigations of the CuA centre of nitrous oxide reductase from Pseudomonas stutzeri by site-directed mutagenesis and X-ray absorption spectroscopy.
  Eur J Biochem, 267, 1368-1381.  
10775261 T.Soulimane, G.Buse, G.P.Bourenkov, H.D.Bartunik, R.Huber, and M.E.Than (2000).
Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus.
  EMBO J, 19, 1766-1776.
PDB code: 1ehk
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 code is shown on the right.