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(-) Description

Title :  CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES IN THE REDUCED STATE BOUND WITH CYANIDE
 
Authors :  L. Qin, D. A. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller
Date :  22 Jan 09  (Deposition) - 16 Jun 09  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Conformational Changes, Cyanide Binding, Cell Membrane, Copper, Electron Transport, Heme, Hydrogen Ion Transport, Ion Transport, Iron, Membrane, Metal-Binding, Oxidoreductase, Respiratory Chain, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Qin, J. Liu, D. Mills, D. A. Proshlyakov, C. Hiser, S. Ferguson-Miller
Redox Dependent Conformational Changes In Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake.
Biochemistry V. 48 5121 2009
PubMed-ID: 19397279  |  Reference-DOI: 10.1021/BI9001387
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C OXIDASE SUBUNIT 1
    Chains: A, C
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRK415
    Expression System Strain: DELTAIDELTAIV
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: CTAD
    Organism Common: RHODOPSEUDOMONAS SPHAEROIDES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: CYTOCHROME C OXIDASE POLYPEPTIDE I, CYTOCHROME AA3 SUBUNIT 1
 
Molecule 2 - CYTOCHROME C OXIDASE SUBUNIT 2
    Chains: B, D
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: RHODOBACTER SPHAEROIDES
    Expression System Plasmid: PRK415
    Expression System Strain: DELTAIDELTAIV
    Expression System Taxid: 1063
    Expression System Vector Type: PLASMID
    Gene: CTAC, COXII, CTAB
    Organism Common: RHODOPSEUDOMONAS SPHAEROIDES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: CYTOCHROME C OXIDASE POLYPEPTIDE II, CYTOCHROME AA3 SUBUNIT 2, OXIDASE AA(3) SUBUNIT 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 43)

Asymmetric Unit (9, 43)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CD4Ligand/IonCADMIUM ION
3CU16Ligand/IonCOPPER (I) ION
4CYN2Ligand/IonCYANIDE ION
5DMU10Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
6HEA4Ligand/IonHEME-A
7HTO1Ligand/IonHEPTANE-1,2,3-TRIOL
8MG2Ligand/IonMAGNESIUM ION
9TRD12Ligand/IonTRIDECANE
Biological Unit 1 (6, 19)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
3CU13Ligand/IonCOPPER (I) ION
4CYN1Ligand/IonCYANIDE ION
5DMU6Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
6HEA2Ligand/IonHEME-A
7HTO1Ligand/IonHEPTANE-1,2,3-TRIOL
8MG-1Ligand/IonMAGNESIUM ION
9TRD6Ligand/IonTRIDECANE
Biological Unit 2 (5, 16)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
3CU13Ligand/IonCOPPER (I) ION
4CYN1Ligand/IonCYANIDE ION
5DMU4Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
6HEA2Ligand/IonHEME-A
7HTO-1Ligand/IonHEPTANE-1,2,3-TRIOL
8MG-1Ligand/IonMAGNESIUM ION
9TRD6Ligand/IonTRIDECANE

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:34 , GLY A:38 , VAL A:45 , THR A:48 , MET A:51 , ARG A:52 , TRP A:95 , ILE A:99 , HIS A:102 , MET A:106 , MET A:107 , GLY A:171 , TRP A:172 , TYR A:414 , PHE A:420 , HIS A:421 , SER A:425 , MET A:460 , PHE A:468 , GLN A:471 , ARG A:481 , ARG A:482 , SER A:504 , HOH A:583 , HOH A:584 , HOH A:650BINDING SITE FOR RESIDUE HEA A 567
02AC2SOFTWARETRP A:172 , VAL A:287 , VAL A:291 , HIS A:333 , HIS A:334 , THR A:352 , ALA A:356 , GLY A:360 , PHE A:364 , PHE A:391 , GLY A:395 , VAL A:396 , GLY A:398 , ILE A:399 , LEU A:401 , SER A:402 , ASP A:407 , HIS A:411 , VAL A:416 , HIS A:419 , PHE A:420 , VAL A:423 , MET A:424 , ARG A:481 , CYN A:572 , HOH A:595 , HOH A:605 , HOH A:634 , HOH A:656 , HOH A:661 , PRO B:108BINDING SITE FOR RESIDUE HEA A 568
03AC3SOFTWAREHIS A:284 , HIS A:333 , HIS A:334 , CYN A:572BINDING SITE FOR RESIDUE CU1 A 569
04AC4SOFTWAREHIS A:411 , ASP A:412 , GLU B:254 , HOH B:318 , HOH B:327 , HOH B:334BINDING SITE FOR RESIDUE MG A 570
05AC5SOFTWAREGLU A:54 , ALA A:57 , GLY A:59 , GLN A:61 , HOH A:628 , HOH A:639BINDING SITE FOR RESIDUE CA A 571
06AC6SOFTWAREHIS A:284 , HIS A:333 , HIS A:334 , HEA A:568 , CU1 A:569BINDING SITE FOR RESIDUE CYN A 572
07AC7SOFTWARETRP A:451 , TYR A:517 , DMU A:574 , GLN B:142 , TRP B:143 , PRO B:164 , HOH B:289 , HOH B:303 , HOH B:308 , HOH B:316BINDING SITE FOR RESIDUE DMU A 573
08AC8SOFTWARETRP A:451 , ALA A:506 , DMU A:573 , TRD A:582 , HOH A:681BINDING SITE FOR RESIDUE DMU A 574
09AC9SOFTWARETRP A:20 , VAL A:31 , MET A:443 , SER A:444BINDING SITE FOR RESIDUE DMU A 575
10BC1SOFTWAREMET A:56 , ALA A:57 , GLN A:61 , SER A:83 , ALA A:84 , VAL A:85 , PHE A:505 , TRD A:577 , HOH A:639 , HOH A:687BINDING SITE FOR RESIDUE DMU A 576
11BC2SOFTWARELEU A:80 , TRP A:81 , DMU A:576BINDING SITE FOR RESIDUE TRD A 577
12BC3SOFTWAREARG A:476 , THR B:41BINDING SITE FOR RESIDUE TRD A 578
13BC4SOFTWAREMET A:350BINDING SITE FOR RESIDUE TRD A 579
14BC5SOFTWAREDMU A:574BINDING SITE FOR RESIDUE TRD A 582
15BC6SOFTWAREGLU B:152 , ALA B:276 , GLU B:280 , HOH B:291 , ALA D:276 , GLU D:280 , HIS D:283 , HOH D:1327 , HOH D:1328BINDING SITE FOR RESIDUE HTO B 1
16BC7SOFTWARECU1 B:4 , CYS B:252 , GLU B:254 , CYS B:256 , HIS B:260BINDING SITE FOR RESIDUE CU1 B 3
17BC8SOFTWARECU1 B:3 , HIS B:217 , CYS B:252 , CYS B:256 , MET B:263BINDING SITE FOR RESIDUE CU1 B 4
18BC9SOFTWAREGLU B:280 , HIS B:283 , HIS B:285 , GLU D:152BINDING SITE FOR RESIDUE CD B 8
19CC1SOFTWAREHIS B:96 , GLU B:101 , HOH B:386BINDING SITE FOR RESIDUE CD B 9
20CC2SOFTWAREPHE A:364 , TRP A:371 , LEU B:75 , PHE B:94 , HIS B:96 , ASN B:97 , LEU B:100 , TRP B:104 , GLU C:86 , SER D:173 , PRO D:174 , GLU D:177 , HOH D:1151BINDING SITE FOR RESIDUE DMU B 288
21CC3SOFTWARELEU C:34 , GLY C:38 , VAL C:45 , THR C:48 , MET C:51 , ARG C:52 , TRP C:95 , ILE C:99 , HIS C:102 , MET C:106 , MET C:107 , VAL C:111 , GLY C:171 , TRP C:172 , TYR C:414 , PHE C:420 , HIS C:421 , MET C:424 , SER C:425 , VAL C:429 , MET C:460 , PHE C:468 , GLN C:471 , ARG C:482 , SER C:504 , PHE C:508 , HOH C:1003 , HOH C:1011 , HOH C:1130BINDING SITE FOR RESIDUE HEA C 567
22CC4SOFTWARELEU B:120 , PRO B:121 , PHE B:124 , GLU B:128BINDING SITE FOR RESIDUE DMU B 11
23CC5SOFTWARETRP C:172 , VAL C:287 , VAL C:291 , HIS C:333 , THR C:352 , ALA C:356 , GLY C:360 , PHE C:364 , PHE C:391 , GLY C:395 , VAL C:396 , GLY C:398 , ILE C:399 , LEU C:401 , SER C:402 , ASP C:407 , HIS C:411 , VAL C:416 , HIS C:419 , PHE C:420 , VAL C:423 , MET C:424 , ARG C:481 , CYN C:572 , HOH C:1015 , HOH C:1030 , HOH C:1096 , HOH C:1142 , HOH C:1157 , PRO D:108BINDING SITE FOR RESIDUE HEA C 568
24CC6SOFTWAREHIS C:284 , HIS C:333 , HIS C:334 , CYN C:572BINDING SITE FOR RESIDUE CU1 C 569
25CC7SOFTWAREHIS C:411 , ASP C:412 , GLU D:254 , HOH D:1071 , HOH D:1082 , HOH D:1094BINDING SITE FOR RESIDUE MG C 570
26CC8SOFTWAREGLU C:54 , ALA C:57 , GLY C:59 , GLN C:61 , HOH C:1085 , HOH C:1107BINDING SITE FOR RESIDUE CA C 571
27CC9SOFTWAREHIS C:284 , HIS C:333 , HIS C:334 , HEA C:568 , CU1 C:569BINDING SITE FOR RESIDUE CYN C 572
28DC1SOFTWARETRP C:451 , GLY C:513BINDING SITE FOR RESIDUE TRD C 1001
29DC2SOFTWARETRP C:451 , HOH C:1102BINDING SITE FOR RESIDUE DMU C 1002
30DC3SOFTWAREMET C:56 , ALA C:57 , GLN C:61 , SER C:83 , PHE C:502 , PHE C:505 , TRD C:1006 , HOH C:1107 , HOH C:1364 , HOH C:1612BINDING SITE FOR RESIDUE DMU C 1005
31DC4SOFTWARELEU C:80 , TRP C:81 , PRO C:82 , DMU C:1005BINDING SITE FOR RESIDUE TRD C 1006
32DC5SOFTWAREPHE C:473BINDING SITE FOR RESIDUE TRD C 1009
33DC6SOFTWARECU1 D:4 , CYS D:252 , GLU D:254 , CYS D:256 , HIS D:260BINDING SITE FOR RESIDUE CU1 D 3
34DC7SOFTWARECU1 D:3 , HIS D:217 , CYS D:252 , CYS D:256 , MET D:263BINDING SITE FOR RESIDUE CU1 D 4
35DC8SOFTWAREGLU B:152 , GLU D:280 , HIS D:283 , HIS D:285BINDING SITE FOR RESIDUE CD D 8
36DC9SOFTWAREHIS D:96 , GLU D:101BINDING SITE FOR RESIDUE CD D 9
37EC1SOFTWARETRP C:371 , PHE D:71 , LEU D:75 , PHE D:94 , HIS D:96 , ASN D:97 , TRP D:104BINDING SITE FOR RESIDUE DMU D 1003
38EC2SOFTWAREARG C:476 , THR D:41BINDING SITE FOR RESIDUE TRD D 1007
39EC3SOFTWAREPRO D:121 , GLU D:128BINDING SITE FOR RESIDUE DMU D 1011

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:64 -A:88
2C:64 -C:88

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:176 -Pro A:177
2Ser A:544 -Pro A:545
3Gln B:142 -Trp B:143
4Pro C:176 -Pro C:177
5Ser C:544 -Pro C:545
6Gln D:142 -Trp D:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FYI)

(-) PROSITE Motifs  (5, 10)

Asymmetric Unit (5, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1_RHOSH20-558
 		  2A:20-551
C:20-550
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_RHOSH35-130
 		  2B:35-130
D:35-130
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_RHOSH131-281
 		  2B:131-281
D:131-281
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_RHOSH215-263
 		  2B:215-263
D:215-263
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1_RHOSH280-334
 		  2A:280-334
C:280-334
Biological Unit 1 (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1_RHOSH20-558
 		  1A:20-551
-
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_RHOSH35-130
 		  1B:35-130
-
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_RHOSH131-281
 		  1B:131-281
-
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_RHOSH215-263
 		  1B:215-263
-
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1_RHOSH280-334
 		  1A:280-334
-
Biological Unit 2 (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COX1PS50855 Cytochrome oxidase subunit I profile.COX1_RHOSH20-558
 		  1-
C:20-550
2COX2_TMPS50999 Cytochrome oxidase subunit II transmembrane region profile.COX2_RHOSH35-130
 		  1-
D:35-130
3COX2_CUAPS50857 Cytochrome oxidase subunit II copper A binding domain profile.COX2_RHOSH131-281
 		  1-
D:131-281
4COX2PS00078 CO II and nitrous oxide reductase dinuclear copper centers signature.COX2_RHOSH215-263
 		  1-
D:215-263
5COX1_CUBPS00077 Heme-copper oxidase catalytic subunit, copper B binding region signature.COX1_RHOSH280-334
 		  1-
C:280-334

(-) Exons   (0, 0)

(no "Exon" information available for 3FYI)

(-) 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:535
 aligned with COX1_RHOSH | P33517 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:535
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546     
           COX1_RHOSH    17 FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 551
               SCOP domains d3fyia_ A: Bacterial aa3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3fyiA00 A:17-551 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee............hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---COX1  PDB: A:20-551 UniProt: 20-558                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: A:280-334 UniProt: 280-334              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fyi A  17 FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF 551
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546     


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with COX2_RHOSH | Q03736 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:256
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      
           COX2_RHOSH    30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGG 285
               SCOP domains d3fyib1 B:30-129 Bacterial aa3 type cytochrome c oxidase subunit II                                 d3fyib2 B:130-285 Cytochrome c oxidase                                                                                                                       SCOP domains
               CATH domains -----3fyiB01 B:35-130  [code=1.10.287.90, no name defined]                                           3fyiB02 B:131-283 Cupredoxins -  blue copper proteins                                                                                                    -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeeee....eeeee....hhhhh.....hhhhhhhhhhh..hhhhh.......eeee...eeeeeeee....eeeeehhhheeeee.....eeeeee....eeeee........hhhhh.eeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----COX2_TM  PDB: B:35-130 UniProt: 35-130                                                          COX2_CUA  PDB: B:131-281 UniProt: 131-281                                                                                                              ---- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: B:215-263 UniProt: 215-263            ---------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fyi B  30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHH 285
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      


Chain C from PDB  Type:PROTEIN  Length:531
 aligned with COX1_RHOSH | P33517 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:531
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549 
           COX1_RHOSH    20 WFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHT 550
               SCOP domains d3fyic_ C: Bacterial aa3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3fyiC00 C:20-550 Cytochrome C Oxidase, chain A                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....hhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) COX1  PDB: C:20-550 UniProt: 20-558                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX1_CUB  PDB: C:280-334 UniProt: 280-334              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fyi C  20 WFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAEHLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQLGSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMRAPGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQPSGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPMVYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIKIFSWIATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYVVAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANLTFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIFYTLTRGARVTANNYWNEHADTLEWTLTSPPPEHT 550
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549 


Chain D from PDB  Type:PROTEIN  Length:256
 aligned with COX2_RHOSH | Q03736 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:256
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      
           COX2_RHOSH    30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQARGG 285
               SCOP domains d3fyid1 D:30-129 Bacterial aa3 type cytochrome c oxidase subunit II                                 d3fyid2 D:130-285 Cytochrome c oxidase                                                                                                                       SCOP domains
               CATH domains -----3fyiD01 D:35-130  [code=1.10.287.90, no name defined]                                           3fyiD02 D:131-283 Cupredoxins -  blue copper proteins                                                                                                    -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee..eeeee......eeee....hhhhh.....hhhhhhhhhhh..hhhhh.......eeee...eeeeeeee....eeeeehhhheeeee.....eeeeee....eeeee........hhhhh.eeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----COX2_TM  PDB: D:35-130 UniProt: 35-130                                                          COX2_CUA  PDB: D:131-281 UniProt: 131-281                                                                                                              ---- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: D:215-263 UniProt: 215-263            ---------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fyi D  30 LEIIGRPQPGGTGFQPSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAWTIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSPATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAFGVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQHHHH 285
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
   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  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FYI)

(-) Gene Ontology  (19, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (COX1_RHOSH | P33517)
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: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:0022900    electron transport chain    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: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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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,D   (COX2_RHOSH | Q03736)
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:0022900    electron transport chain    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: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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  COX2_RHOSH | Q03736
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        COX1_RHOSH | P33517: 1m56 1m57 2gsm 3dtu 3fye
        COX2_RHOSH | Q03736: 1m56 1m57 2gsm 3dtu 3fye

(-) Related Entries Specified in the PDB File

2gsm CATALYTIC CORE (SUBUNITS I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES
3fye CATALYTIC CORE SUBUNITS (I AND II) OF CYTOCHROME C OXIDASE FROM RHODOBACTER SPHAEROIDES IN THE REDUCED STATE