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(-) Description

Title :  STRUCTURE OF RECOMBINANT CYTOCHROME BA3 OXIDASE MUTANT Y133W+T231F FROM THERMUS THERMOPHILUS
 
Authors :  Y. Li, Y. Chen, C. D. Stout
Date :  20 Aug 12  (Deposition) - 16 Jan 13  (Release) - 13 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oxidoreductase, Proton Pump (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Mcdonald, C. Funatogawa, Y. Li, I. Szundi, Y. Chen, J. A. Fee, C. D. Stout, O. Einarsdottir
Ligand Access To The Active Site In Thermus Thermophilusba(3) And Bovine Heart Aa(3) Cytochrome Oxidases.
Biochemistry V. 52 640 2013
PubMed-ID: 23282175  |  Reference-DOI: 10.1021/BI301358A

(-) Compounds

Molecule 1 - CYTOCHROME C OXIDASE SUBUNIT 1
    Chains: A
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: THERMUS THERMOPHILUS
    Expression System Plasmid: PMK18
    Expression System Strain: MT111
    Expression System Taxid: 274
    Expression System Vector Type: PLASMID
    Gene: CBAA, TTHA1135
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579
    Synonym: CYTOCHROME C BA(3) SUBUNIT I, CYTOCHROME C OXIDASE POLYPEPTIDE I, CYTOCHROME CBA3 SUBUNIT 1
 
Molecule 2 - CYTOCHROME C OXIDASE SUBUNIT 2
    Chains: B
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: THERMUS THERMOPHILUS
    Expression System Plasmid: PMK18
    Expression System Strain: MT111
    Expression System Taxid: 274
    Expression System Vector Type: PLASMID
    Gene: CBAB, CTAC, TTHA1134
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579
    Synonym: CYTOCHROME C BA(3) SUBUNIT II, CYTOCHROME C OXIDASE POLYPEPTIDE II, CYTOCHROME CBA3 SUBUNIT 2
 
Molecule 3 - CYTOCHROME C OXIDASE POLYPEPTIDE 2A
    Chains: C
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: THERMUS THERMOPHILUS
    Expression System Plasmid: PMK18
    Expression System Strain: MT111
    Expression System Taxid: 274
    Expression System Vector Type: PLASMID
    Gene: CBAD, TTHA1133
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579
    Synonym: CYTOCHROME C BA(3) SUBUNIT IIA, CYTOCHROME C OXIDASE POLYPEPTIDE IIA, CYTOCHROME CBA3 SUBUNIT 2A

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric/Biological Unit (6, 21)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2CUA1Ligand/IonDINUCLEAR COPPER ION
3HAS1Ligand/IonHEME-AS
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5OLC16Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6PER1Ligand/IonPEROXIDE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:233 , HIS A:282 , HIS A:283 , PER A:604BINDING SITE FOR RESIDUE CU A 601
02AC2SOFTWARELEU A:32 , GLY A:39 , GLN A:42 , ALA A:43 , TYR A:46 , TYR A:65 , HIS A:72 , ASN A:76 , ALA A:77 , LEU A:132 , TRP A:133 , PHE A:385 , HIS A:386 , 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:713 , HOH A:717BINDING SITE FOR RESIDUE HEM A 602
03AC3SOFTWARETRP 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 , ALA A:317 , LEU A:320 , LEU A:353 , 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 , VAL A:389 , ARG A:449 , PER A:604 , HOH A:701 , HOH A:721 , HOH A:742 , HOH A:743BINDING SITE FOR RESIDUE HAS A 603
04AC4SOFTWAREHIS A:233 , VAL A:236 , HIS A:283 , CU A:601 , HAS A:603BINDING SITE FOR RESIDUE PER A 604
05AC5SOFTWAREVAL A:437 , HIS A:440 , OLC A:606 , OLC B:202 , PHE C:22 , GLY C:25 , ALA C:28BINDING SITE FOR RESIDUE OLC A 605
06AC6SOFTWARELEU A:354 , OLC A:605 , OLC B:202 , THR C:18BINDING SITE FOR RESIDUE OLC A 606
07AC7SOFTWAREVAL A:158 , TYR A:161 , OLC A:616BINDING SITE FOR RESIDUE OLC A 607
08AC8SOFTWARELEU A:147 , PHE A:213 , LEU A:215 , TRP A:341 , TRP A:426 , OLC A:610 , OLC A:614 , OLC A:615 , OLC A:616BINDING SITE FOR RESIDUE OLC A 608
09AC9SOFTWAREPRO A:292 , THR A:293 , VAL A:300 , PHE A:304BINDING SITE FOR RESIDUE OLC A 609
10BC1SOFTWARELYS A:140 , TRP A:143 , PHE A:213 , LEU A:430 , OLC A:608 , OLC A:617BINDING SITE FOR RESIDUE OLC A 610
11BC2SOFTWARETRP A:111 , OLC A:614BINDING SITE FOR RESIDUE OLC A 611
12BC3SOFTWARETYR A:161 , ASP A:165 , ARG A:168 , OLC A:613BINDING SITE FOR RESIDUE OLC A 612
13BC4SOFTWARETRP A:167 , ARG A:168 , GLY A:528 , PHE A:531 , OLC A:612BINDING SITE FOR RESIDUE OLC A 613
14BC5SOFTWAREGLY A:104 , LEU A:108 , ALA A:464 , PHE A:469 , OLC A:608 , OLC A:611 , OLC A:615 , OLC A:617BINDING SITE FOR RESIDUE OLC A 614
15BC6SOFTWAREGLY A:47 , ASN A:48 , MET A:112 , VAL A:151 , VAL A:471 , LEU A:472 , OLC A:608 , OLC A:614BINDING SITE FOR RESIDUE OLC A 615
16BC7SOFTWAREVAL A:216 , ASP A:415 , OLC A:607 , OLC A:608BINDING SITE FOR RESIDUE OLC A 616
17BC8SOFTWAREARG A:337 , TRP A:341 , OLC A:610 , OLC A:614BINDING SITE FOR RESIDUE OLC A 617
18BC9SOFTWAREHIS B:114 , CYS B:149 , GLN B:151 , CYS B:153 , HIS B:157 , MET B:160BINDING SITE FOR RESIDUE CUA B 201
19CC1SOFTWARETRP A:441 , OLC A:605 , OLC A:606 , HOH A:705 , ARG B:141 , GLU B:144 , TYR B:145 , ARG C:33BINDING SITE FOR RESIDUE OLC B 202
20CC2SOFTWAREALA B:13 , TYR B:14 , GLY B:17 , PHE B:21 , TYR B:35 , OLC C:101BINDING SITE FOR RESIDUE OLC B 203
21CC3SOFTWAREVAL B:28 , LEU B:32 , TYR B:35 , OLC B:203 , PHE C:31BINDING SITE FOR RESIDUE OLC C 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GP8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:137 -Pro A:138
2Ala B:87 -Phe B:88
3Gln B:91 -Pro B:92
4Asn B:93 -Pro B:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GP8)

(-) Exons   (0, 0)

(no "Exon" information available for 4GP8)

(-) Sequences/Alignments

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:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4gp8a_ A: Bacterial ba3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gp8 A  15 YPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWMAFIGLVVAALPLLANEATVLWTFYPPLKGHWAFYLGASVFVLSTWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWSFGLVEGVDPLVARTLFWWFGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFPLPFAEVIDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW 562
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    || 509  ||   523       533       543       553         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    489|    512|                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     505     517                                             


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d4gp8b1 B:3-40                        d4gp8b2 B:41-168 Cytochrome c oxidase                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhh.eeeee..eeeeeeeee..eee...eeee...eeeeeee.....eeeee.....eeee.....eeeeee....eeeeee.......hhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gp8 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:31
                                                               
               SCOP domains d4gp8c_ 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
                 4gp8 C   4 KPKGALAVILVLTLTILVFWLGVYAVFFARG  34
                                    13        23        33
   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  (4, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GP8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GP8)

(-) Gene Ontology  (18, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  4gp8
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 Related Entries

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

UniProtKB/Swiss-Prot
        COX1_THET8 | Q5SJ79: 1ehk 2qpd 2qpe 3bvd 3eh3 3eh4 3eh5 3qjq 3qjr 3qjs 3qjt 3qju 3qjv 3s33 3s38 3s39 3s3a 3s3b 3s3c 3s3d 3s8f 3s8g 4fa7 4faa 4g70 4g71 4g72 4g7q 4g7r 4g7s 4gp4 4gp5 4n4y
        COX2_THET8 | Q5SJ80: 1ehk 2qpd 2qpe 3bvd 3eh3 3eh4 3eh5 3qjq 3qjr 3qjs 3qjt 3qju 3qjv 3s33 3s38 3s39 3s3a 3s3b 3s3c 3s3d 3s8f 3s8g 4fa7 4faa 4g70 4g71 4g72 4g7q 4g7r 4g7s 4gp4 4gp5 4n4y
        COXA_THET8 | P82543: 1ehk 1xme 2qpd 2qpe 3bvd 3eh3 3eh4 3eh5 3qjq 3qjr 3qjs 3qjt 3qju 3qjv 3s33 3s38 3s39 3s3a 3s3b 3s3c 3s3d 3s8f 3s8g 4fa7 4faa 4g70 4g71 4g72 4g7q 4g7r 4g7s 4gp4 4gp5 4n4y

(-) Related Entries Specified in the PDB File

4g70 4g71 4g72 4g7q 4g7r 4g7s 4gp4 4gp5