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Title :   STRUCTURE OF RECOMBINANT CYTOCHROME BA3 OXIDASE FROM THERMUS THERMOPHILUS

Authors :   L. M. Hunsicker-Wang, R. L. Pacoma, Y. Chen, J. A. Fee, C. D. Stout

Date :   01 Oct 04 (Deposition) - 22 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Cytochrome Oxidase, Heme, Heme-As, Integral Membrane Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. M. Hunsicker-Wang, R. L. Pacoma, Y. Chen, J. A. Fee, C. D. Stout
A Novel Cryoprotection Scheme For Enhancing The Diffraction Of Crystals Of Recombinant Cytochrome Ba3 Oxidase From Thermus Thermophilus.
Acta Crystallogr. , Sect. D V. 61 340 2005
PubMed-ID: 15735345 | Reference-DOI: 10.1107/S0907444904033906

Molecule 1 - CYTOCHROME C OXIDASE POLYPEPTIDE I
	Chains	:	A
	EC Number	:	1.9.3.1
	Engineered	:	YES
	Expression System	:	THERMUS THERMOPHILUS HB8
	Expression System Plasmid	:	PMK18
	Expression System Strain	:	HB8
	Expression System Taxid	:	300852
	Expression System Vector Type	:	PLASMID
	Gene	:	CBAA
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	CYTOCHROME C BA(3), SUBUNIT I, CYTOCHROME CBA3 SUBUNIT 1

Molecule 2 - CYTOCHROME C OXIDASE POLYPEPTIDE II
	Chains	:	B
	EC Number	:	1.9.3.1
	Engineered	:	YES
	Expression System	:	THERMUS THERMOPHILUS HB8
	Expression System Plasmid	:	PMK18
	Expression System Strain	:	HB8
	Expression System Taxid	:	300852
	Expression System Vector Type	:	PLASMID
	Gene	:	CBAB, CTAC
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	CYTOCHROME C BA(3), SUBUNIT II, CYTOCHROME CBA3 SUBUNIT 2

Molecule 3 - CYTOCHROME C OXIDASE POLYPEPTIDE IIA
	Chains	:	C
	EC Number	:	1.9.3.1
	Engineered	:	YES
	Expression System	:	THERMUS THERMOPHILUS HB8
	Expression System Plasmid	:	PMK18
	Expression System Strain	:	HB8
	Expression System Taxid	:	300852
	Expression System Vector Type	:	PLASMID
	Gene	:	CBAD
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	CYTOCHROME C BA(3), SUBUNIT IIA, CYTOCHROME CBA3 SUBUNIT 2A

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 6)

No.	Name	Count	Type	Full Name
1	BNG	1	Ligand/Ion	B-NONYLGLUCOSIDE
2	CU	1	Ligand/Ion	COPPER (II) ION
3	CUA	1	Ligand/Ion	DINUCLEAR COPPER ION
4	GOL	1	Ligand/Ion	GLYCEROL
5	HAS	1	Ligand/Ion	HEME-AS
6	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:19 , TYR A:23 , TRP A:107 , LEU A:108 , TRP A:111	BINDING SITE FOR RESIDUE BNG A 805
2	AC2	SOFTWARE	HIS A:233 , HIS A:282 , HIS A:283 , HOH A:867	BINDING SITE FOR RESIDUE CU A 803
3	AC3	SOFTWARE	GLY A:39 , PRO A:40 , GLN A:42 , ALA A:43 , TYR A:46 , TYR A:65 , LEU A:69 , HIS A:72 , ASN A:76 , ALA A:77 , LEU A:132 , TYR A:133 , PHE A:385 , HIS A:386 , VAL A:389 , ALA A:390 , THR A:394 , MET A:432 , MET A:435 , ARG A:449 , ARG A:450 , ALA A:451 , LEU A:477 , HOH A:808 , HOH A:834	BINDING SITE FOR RESIDUE HEM A 800
4	AC4	SOFTWARE	TYR A:133 , TRP A:229 , VAL A:236 , TYR A:237 , HIS A:282 , HIS A:283 , SER A:309 , LEU A:310 , ALA A:313 , TRP A:335 , LEU A:353 , LEU A:354 , PHE A:356 , GLY A:360 , GLY A:363 , ASN A:366 , ALA A:367 , ASP A:372 , HIS A:376 , HIS A:384 , PHE A:385 , GLN A:388 , ARG A:449 , GOL A:804 , HOH A:832 , HOH A:833 , HOH A:848 , HOH A:867 , VAL C:11	BINDING SITE FOR RESIDUE HAS A 801
5	AC5	SOFTWARE	HIS B:114 , CYS B:149 , GLN B:151 , CYS B:153 , HIS B:157 , MET B:160	BINDING SITE FOR RESIDUE CUA B 802
6	AC6	SOFTWARE	TYR A:136 , ARG A:225 , HIS A:283 , HIS A:376 , ASN A:377 , ARG A:449 , ARG A:450 , HAS A:801 , GLU B:126 , GLN B:151	BINDING SITE FOR RESIDUE GOL A 804

(no "SS Bond" information available for 1XME)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:137	-	Pro A:138
2	Gln B:91	-	Pro B:92
3	Asn B:93	-	Pro B:94

(no "SAP(SNP)/Variant" information available for 1XME)

Asymmetric/Biological Unit (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

(no "Exon" information available for 1XME)

Asymmetric/Biological 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:557
 aligned with COX1_THETH | Q56408 from UniProtKB/Swiss-Prot  Length:108

    Alignment length:557
                                                                                                                                                                                                                                                                                                                                                                      1                                                                                                        108                                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70        80        90       100       | -         -         -         -         -         -         -         -         -         -         -         -       
           COX1_THETH     - ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAG-----------------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1xmea_ A: Bacterial ba3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1xmeA00 A:6-562 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xme A   6 SEISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW 562
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with COX2_THETH | P98052 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:166
                                                           1                                                                                                                                      
                                     -         -         - |       9        19        29        39        49        59        69        79        89        99       109       119       129      
           COX2_THETH     - -------------------------------AYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE 135
               SCOP domains d1xmeb2 B:3-40                        d1xmeb1 B:41-168 Cytochrome c oxidase                                                                                            SCOP domains
               CATH domains 1xmeB01 B:3-46                              1xmeB02 B:47-168 Cupredoxins -  blue copper proteins                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhh.eee....eeeeeeeee..eee...eeee...eeeeeee.....eeeee.....eeee.....eeeeee....eeeeee.......hhhh.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
                 1xme B   3 DEHKAHKAILAYEKGWLAFSLAMLFVFIALIAYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE 168
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain C from PDB  Type:PROTEIN  Length:33
 aligned with COXA_THET8 | P82543 from UniProtKB/Swiss-Prot  Length:34

    Alignment length:33
                                    11        21        31   
           COXA_THET8     2 EEKPKGALAVILVLTLTILVFWLGVYAVFFARG  34
               SCOP domains d1xmec_ C:                        SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 1xme C   2 EEKPKGALAVILVLTLTILVFWLGVYAVFFARG  34
                                    11        21        31

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 '\|'

(no "Pfam Domain" information available for 1XME)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (COX1_THETH | Q56408)

molecular function
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0009060	aerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
	GO:0006119	oxidative phosphorylation	The phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
	GO:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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.

Chain 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.

Chain C (COXA_THET8 | P82543)

molecular function
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	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:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
	GO:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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