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(-) Description

Title :  CRYSTAL STRUCTURE OF FLAVOCYTOCHROME C FROM THERMOCHROMATIUM TEPIDUM
 
Authors :  Y. Hirano, Y. Kimura, H. Suzuki, K. Miki, Z. -Y. Wang
Date :  09 Apr 12  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sulfide Oxidation, Heme C Binding, Fad Binding, Electron Transport- Oxidoreductase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hirano, Y. Kimura, H. Suzuki, K. Miki, Z. -Y. Wang
Structure Analysis And Comparative Characterization Of The Cytochrome C' And Flavocytochrome C From Thermophilic Purpl Photosynthetic Bacterium Thermochromatium Tepidum
Biochemistry V. 51 6556 2012
PubMed-ID: 22827326  |  Reference-DOI: 10.1021/BI3005522

(-) Compounds

Molecule 1 - FLAVOCYTOCHROME C HEME SUBUNIT
    Chains: A
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050
    Synonym: FCCA SUBUNIT
 
Molecule 2 - FLAVOCYTOCHROME C FLAVIN SUBUNIT
    Chains: B
    Organism Scientific: THERMOCHROMATIUM TEPIDUM
    Organism Taxid: 1050
    Synonym: FCCB SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1CSS2Mod. Amino AcidS-MERCAPTOCYSTEINE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL3Ligand/IonGLYCEROL
4HEC2Ligand/IonHEME C
5NO32Ligand/IonNITRATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:11 , CYS A:14 , HIS A:15 , PHE A:37 , VAL A:40 , MET A:41 , PHE A:44 , SER A:51 , THR A:52 , ILE A:53 , MET A:54 , MET A:69 , TYR A:128 , HEC A:202 , GOL A:203 , HOH A:320 , TYR B:306 , LEU B:334 , THR B:336 , TYR B:338 , TYR B:387 , HOH B:601BINDING SITE FOR RESIDUE HEC A 201
2AC2SOFTWARETYR A:100 , CYS A:101 , CYS A:104 , HIS A:105 , HIS A:119 , LEU A:121 , TYR A:128 , PHE A:136 , ARG A:141 , MET A:143 , GLU A:144 , LYS A:146 , MET A:147 , LEU A:154 , HEC A:201 , HOH A:302 , HOH A:307 , HOH A:337 , HOH A:380 , HOH A:455 , HOH A:478BINDING SITE FOR RESIDUE HEC A 202
3AC3SOFTWAREPHE A:44 , TYR A:128 , ALA A:132 , ASP A:135 , ARG A:141 , HEC A:201 , ARG B:383 , HOH B:601BINDING SITE FOR RESIDUE GOL A 203
4AC4SOFTWAREPRO A:2 , GLY A:60 , ASP A:65 , HOH A:301 , HOH A:390 , HOH A:428 , VAL B:365BINDING SITE FOR RESIDUE GOL A 204
5AC5SOFTWAREARG A:137 , LEU A:155 , GLU B:54 , ALA B:56 , SER B:57 , HOH B:793BINDING SITE FOR RESIDUE NO3 A 205
6AC6SOFTWAREVAL B:8 , GLY B:9 , GLY B:11 , THR B:12 , GLY B:13 , ILE B:33 , GLU B:34 , PRO B:35 , ASN B:36 , TYR B:39 , CYS B:42 , TYR B:43 , SER B:76 , ALA B:77 , ALA B:103 , PRO B:104 , GLY B:105 , TRP B:128 , ARG B:160 , CSS B:161 , ARG B:168 , ILE B:261 , GLY B:293 , ASP B:294 , LYS B:303 , SER B:304 , ALA B:305 , TYR B:306 , ALA B:308 , TYR B:338 , TRP B:391 , HOH B:602 , HOH B:603 , HOH B:604 , HOH B:618 , HOH B:667 , HOH B:683 , HOH B:700 , HOH B:709 , HOH B:715 , HOH B:722 , HOH B:765 , HOH B:908 , HOH B:959BINDING SITE FOR RESIDUE FAD B 501
7AC7SOFTWAREALA A:138 , ARG A:140 , HOH A:330 , LEU B:55 , GLU B:142 , HOH B:609 , HOH B:627BINDING SITE FOR RESIDUE GOL B 502
8AC8SOFTWARELEU B:207 , ALA B:342 , PRO B:343 , GLY B:344 , TYR B:345 , HOH B:920 , HOH B:941BINDING SITE FOR RESIDUE NO3 B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VRD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:23 -Pro A:24
2Pro B:157 -Pro B:158
3Gly B:222 -Pro B:223
4Ala B:299 -Pro B:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VRD)

(-) Exons   (0, 0)

(no "Exon" information available for 3VRD)

(-) 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:174
 aligned with D0G7Q3_THETI | D0G7Q3 from UniProtKB/TrEMBL  Length:199

    Alignment length:174
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    
         D0G7Q3_THETI    26 EPTAEMLANNCAGCHGTRGNSAGPASPSIAQMDPAVFVEVMEQFKSGEIQSTIMGRIAKGYSTADFQKMAEYFKQQTYQPVKQSFDKALVAKGTKLHDKYCEKCHVESGKPLADQDEYHILAGQWTPYLRYAIEDFRAERRPMEKKMASKLKELLKAEGEDGLDALFAFYASQQ 199
               SCOP domains d3vrda1 A:1-80 automated matches                                                d3vrda2 A:81-174 automated matches                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhh.hhhhhhhhhh............hhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh...hhhhhh..............hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vrd A   1 EPTAEMLANNCAGCHGTRGNSAGPASPSIAQMDPAVFVEVMEQFKSGEIQSTIMGRIAKGYSTADFQKMAEYFKQQTYQPVKQSFDKALVAKGTKLHDKYCEKCHVESGKPLADQDEYHILAGQWTPYLRYAIEDFRAERRPMEKKMASKLKELLKAEGEDGLDALFAFYASQQ 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with D0G7Q4_THETI | D0G7Q4 from UniProtKB/TrEMBL  Length:431

    Alignment length:400
                                    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
         D0G7Q4_THETI    32 GRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEPNETYYTCYMSNEVIGGDRELASLRVGYDGLRAHGIQVVHDSALGIDPDKKLVKTAGGAEFAYDRCVVAPGIDLLYDKIEGYSEALAAKLPHAWKAGEQTALLRRQLESMDDGGVVIIAPPAPPFRCPPGPYERASQIAHYLKAHKSKSKVIILDNSQTFSKQAQFTKGWERLYGFGTENALIEWHPGPDAAVVKTDTEAMTVETSFGETFKAAVINLIPPQRAGKIAQSASLTNDSGWCPVDIRTFESSLQPGIHVIGDACNAAPMPKSAYSANSQAKVAAAAVVALLKGEEPGTPSYLNTCYSILAPGYGISIAAVYRPNAEGKAIEAVPDSGGITPVDAPDWVLEREVQYAHSWYNNIVHDTFG 431
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh...eeeee.....ee...hhhhhhhh..hhhh.ee.hhhhhhh..eee...eeeee....eeee....eee..eeee...eee.hhhh....hhhhhh.......hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhh........eeee......eeeee....eeee....eee..eeee...eeehhhhhhh.......................eee.hhhh.......hhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee..eeeeeeeeeee......eee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vrd B   2 GRKVVVVGGGTGGATAAKYIKLADPSIEVTLIEPNETYYTCYMSNEVIGGDRELASLRVGYDGLRAHGIQVVHDSALGIDPDKKLVKTAGGAEFAYDRCVVAPGIDLLYDKIEGYSEALAAKLPHAWKAGEQTALLRRQLESMDDGGVVIIAPPAPPFRcPPGPYERASQIAHYLKAHKSKSKVIILDNSQTFSKQAQFTKGWERLYGFGTENALIEWHPGPDAAVVKTDTEAMTVETSFGETFKAAVINLIPPQRAGKIAQSASLTNDSGWCPVDIRTFESSLQPGIHVIGDACNAAPMPKSAYSANSQAKVAAAAVVALLKGEEPGTPSYLNTcYSILAPGYGISIAAVYRPNAEGKAIEAVPDSGGITPVDAPDWVLEREVQYAHSWYNNIVHDTFG 401
                                    11        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
                                                                                                                                                                                         161-CSS                                                                                                                                                                         337-CSS
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VRD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D0G7Q3_THETI | D0G7Q3)
molecular function
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B   (D0G7Q4_THETI | D0G7Q4)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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.

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3vrc