2CUA - JenaLib

Title :   THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS

Authors :   P. A. Williams, N. J. Blackburn, D. Sanders, H. Bellamy, E. A. Stura, J. A. Fee, D. E. Mcree

Date :   18 Feb 99 (Deposition) - 28 May 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Cua Center, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. A. Williams, N. J. Blackburn, D. Sanders, H. Bellamy, E. A. Stura, J. A. Fee, D. E. Mcree
The Cua Domain Of Thermus Thermophilus Ba3-Type Cytochrome C Oxidase At 1. 6 A Resolution.
Nat. Struct. Biol. V. 6 509 1999
PubMed-ID: 10360350 | Reference-DOI: 10.1038/9274
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COX2_CUA	PS50857	Cytochrome oxidase subunit II copper A binding domain profile.	COX2_THETH	33-135	2	A:66-168 B:66-168
2	COX2	PS00078	CO II and nitrous oxide reductase dinuclear copper centers signature.	COX2_THETH	79-127	2	A:112-160 B:112-160

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COX2_CUA	PS50857	Cytochrome oxidase subunit II copper A binding domain profile.	COX2_THETH	33-135	1	A:66-168 -
2	COX2	PS00078	CO II and nitrous oxide reductase dinuclear copper centers signature.	COX2_THETH	79-127	1	A:112-160 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COX2_CUA	PS50857	Cytochrome oxidase subunit II copper A binding domain profile.	COX2_THETH	33-135	1	- B:66-168
2	COX2	PS00078	CO II and nitrous oxide reductase dinuclear copper centers signature.	COX2_THETH	79-127	1	- B:112-160

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:122
 aligned with COX2_THETH | P98052 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:122
                                    23        33        43        53        63        73        83        93       103       113       123       133  
           COX2_THETH    14 AGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE 135
               SCOP domains d2cuaa_ A: Cytochrome c oxidase                                                                                            SCOP domains
               CATH domains 2cuaA00 A:47-168 Cupredoxins -  blue copper proteins                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhh.eeeee..eeeeeeeee..eee...eeee...eeeeeeee....eeee......eeee.....eeeeee....eeeeee............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------COX2_CUA  PDB: A:66-168 UniProt: 33-135                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------COX2  PDB: A:112-160 UniProt: 79-127             -------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cua A  47 AGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE 168
                                    56        66        76        86        96       106       116       126       136       146       156       166

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with COX2_THETH | P98052 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
           COX2_THETH     1 AYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE 135
               SCOP domains d2cuab_ B:    Cytochrome c oxidase                                                                                                      SCOP domains
               CATH domains 2cuaB00 B:   34-168 Cupredoxins -  blue copper proteins                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........---....................hhh.eeeee..eeeeeeeee..eee...eeee...eeeeeee.....eeee......eeee.....eeeeee....eeeeee......hhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------COX2_CUA  PDB: B:66-168 UniProt: 33-135                                                                 PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------COX2  PDB: B:112-160 UniProt: 79-127             -------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cua B  34 AYTLATHTAG---AGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE 168
                                    43   |    53        63        73        83        93       103       113       123       133       143       153       163     
                                    43  47

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A,B (COX2_THETH | P98052)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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	Cis Peptide Bonds
		Ala A:47 - Gly A:48	[ RasMol ]
		Ala A:87 - Phe A:88	[ RasMol ]
		Ala B:87 - Phe B:88	[ RasMol ]
		Asn A:93 - Pro A:94	[ RasMol ]
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		Gln A:91 - Pro A:92	[ RasMol ]
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