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(-) Description

Title :  STRUCTURE OF RECOMBINANT CYTOCHROME BA3 OXIDASE MUTANT V236M FROM THERMUS THERMOPHILUS
 
Authors :  Y. Li, Y. Chen, C. D. Stout
Date :  19 Jul 12  (Deposition) - 24 Jul 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.19
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oxidoreductase, Proton Pump (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, Y. Chen, C. D. Stout
Structure Of Recombinant Cytochrome Ba3 Oxidase Mutant V236 From Thermus Thermophilus
To Be Published
PubMed: search

(-) 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 , HAS A:603 , PER A:604BINDING SITE FOR RESIDUE CU A 601
02AC2SOFTWARELEU A:32 , 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 , ALA A:390 , THR A:394 , MET A:432 , MET A:435 , ARG A:449 , ARG A:450 , ALA A:451 , LEU A:477BINDING SITE FOR RESIDUE HEM A 602
03AC3SOFTWARETYR A:133 , TRP A:229 , MET A:236 , TYR A:237 , TYR A:244 , HIS A:282 , HIS A:283 , SER A:309 , ALA A:313 , VAL A:350 , LEU A:353 , PHE A:356 , 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 , CU A:601 , PER A:604 , HOH A:701 , VAL C:11BINDING SITE FOR RESIDUE HAS A 603
04AC4SOFTWAREHIS A:233 , MET A:236 , HIS A:283 , CU A:601 , HAS A:603BINDING SITE FOR RESIDUE PER A 604
05AC5SOFTWARELEU A:105 , VAL A:158 , TYR A:161 , ILE A:475 , VAL A:479 , OLC A:614BINDING SITE FOR RESIDUE OLC A 605
06AC6SOFTWAREPHE A:213 , LEU A:215 , TRP A:341 , TRP A:426 , OLC A:609 , OLC A:613 , OLC A:614 , OLC A:615BINDING SITE FOR RESIDUE OLC A 606
07AC7SOFTWARETRP A:441 , LEU A:444 , TYR B:145 , HOH B:310 , ARG C:33BINDING SITE FOR RESIDUE OLC A 607
08AC8SOFTWARETHR A:293 , MET A:296 , ILE A:297 , HOH B:301BINDING SITE FOR RESIDUE OLC A 608
09AC9SOFTWARETRP A:143 , SER A:212 , PHE A:213 , GLY A:214 , LEU A:430 , OLC A:606 , OLC A:616BINDING SITE FOR RESIDUE OLC A 609
10BC1SOFTWARETRP A:111 , VAL A:465 , OLC A:613BINDING SITE FOR RESIDUE OLC A 610
11BC2SOFTWARETYR A:161 , ARG A:168BINDING SITE FOR RESIDUE OLC A 611
12BC3SOFTWARETRP A:167 , ARG A:168 , LYS A:171 , GLY A:528BINDING SITE FOR RESIDUE OLC A 612
13BC4SOFTWAREGLY A:104 , LEU A:108 , VAL A:468 , OLC A:606 , OLC A:610 , OLC A:614BINDING SITE FOR RESIDUE OLC A 613
14BC5SOFTWAREGLY A:104 , LEU A:105 , MET A:112 , VAL A:151 , OLC A:605 , OLC A:606 , OLC A:613BINDING SITE FOR RESIDUE OLC A 614
15BC6SOFTWAREASP A:415 , ALA A:416 , ARG A:419 , OLC A:606BINDING SITE FOR RESIDUE OLC A 615
16BC7SOFTWAREARG A:337 , TRP A:341 , PHE A:429 , LEU A:430 , OLC A:609BINDING SITE FOR RESIDUE OLC A 616
17BC8SOFTWAREHIS B:114 , CYS B:149 , GLN B:151 , CYS B:153 , HIS B:157 , MET B:160BINDING SITE FOR RESIDUE CUA B 201
18BC9SOFTWAREPHE B:21 , LEU B:32 , TYR B:35 , OLC B:203BINDING SITE FOR RESIDUE OLC B 202
19CC1SOFTWAREALA B:13 , TYR B:14 , GLY B:17 , TRP B:18 , TYR B:35 , OLC B:202BINDING SITE FOR RESIDUE OLC B 203
20CC2SOFTWAREPHE C:22 , GLY C:25 , VAL C:29 , OLC C:102BINDING SITE FOR RESIDUE OLC C 101
21CC3SOFTWAREOLC C:101BINDING SITE FOR RESIDUE OLC C 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G72)

(-) 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 4G72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G72)

(-) Exons   (0, 0)

(no "Exon" information available for 4G72)

(-) 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:549
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4g72a_ A: Bacterial ba3 type cytochrome c oxidase subunit I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhh....hhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g72 A  12 YEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWMAFIGLVVFALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWSFGLVEGVDPLVARTLFWWTGHPIMYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRKPELAEAPLPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW 562
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491  ||   503       513       523       533       543       553         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            494|                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             497                                                                 


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains d4g72b1 B:3-36 automated matches  d4g72b2 B:37-168 Cytochrome c oxidase                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g72 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 ------------------------------- 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
                 4g72 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  (3, 3)

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 4G72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G72)

(-) Gene Ontology  (18, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  4g72
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  COX1_THET8 | Q5SJ79
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  COXA_THET8 | P82543
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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 4g7q 4g7r 4g7s 4gp4 4gp5 4gp8 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 4g7q 4g7r 4g7s 4gp4 4gp5 4gp8 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 4g7q 4g7r 4g7s 4gp4 4gp5 4gp8 4n4y

(-) Related Entries Specified in the PDB File

4g70 4g71 4g7q 4g7r 4g7s 4gp4 4gp5 4gp8