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(-) Description

Title :  CRYSTAL STRUCTURE OF OCTAHEME CYTOCHROME C FROM SHEWANELLA ONEIDENSIS
 
Authors :  C. G. Mowat, E. Rothery, C. S. Miles, L. Mciver, M. K. Doherty, K. Drewett P. Taylor, M. D. Walkinshaw, S. K. Chapman, G. A. Reid
Date :  16 Mar 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Octaheme, Cytochrome C, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Mowat, E. Rothery, C. S. Miles, L. Mciver, M. K. Doherty, K. Drewette, P. Taylor, M. D. Walkinshaw, S. K. Chapman, G. A. Reid
Octaheme Tetrathionate Reductase Is A Respiratory Enzyme With Novel Heme Ligation.
Nat. Struct. Mol. Biol. V. 11 1023 2004
PubMed-ID: 15361860  |  Reference-DOI: 10.1038/NSMB827

(-) Compounds

Molecule 1 - CYTOCHROME C, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: SHEWANELLA FRIGIDIMARINA
    Expression System Plasmid: PMMB503EH
    Expression System Strain: EG301
    Expression System Taxid: 56812
    Expression System Vector Type: PLASMID
    Gene: SO4144 (TIGR LOCUS)
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1HEM8Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:61 , PHE A:63 , CYS A:64 , LYS A:153 , HEM A:802 , HOH A:1263BINDING SITE FOR RESIDUE SCN A 810
2AC2SOFTWAREASN A:2 , PRO A:3 , HIS A:4 , CYS A:22 , THR A:24 , CYS A:25 , HIS A:26 , CYS A:98 , HIS A:102 , VAL A:131 , ASN A:211 , CYS A:212 , HIS A:213 , ASP A:214 , HEM A:803 , HOH A:1071 , HOH A:1153BINDING SITE FOR RESIDUE HEM A 801
3AC3SOFTWARELYS A:56 , SER A:59 , ASN A:61 , CYS A:64 , ALA A:66 , ILE A:67 , CYS A:74 , CYS A:77 , CYS A:142 , HIS A:143 , TYR A:145 , GLY A:146 , LYS A:153 , HIS A:154 , TRP A:396 , HEM A:804 , HEM A:805 , SCN A:810 , HOH A:884 , HOH A:1076BINDING SITE FOR RESIDUE HEM A 802
4AC4SOFTWAREHIS A:26 , GLN A:29 , ALA A:79 , VAL A:96 , ASP A:97 , CYS A:98 , CYS A:101 , HIS A:102 , GLN A:182 , THR A:187 , HIS A:190 , HEM A:801 , HEM A:804BINDING SITE FOR RESIDUE HEM A 803
5AC5SOFTWARESER A:37 , HIS A:38 , TRP A:41 , LEU A:43 , GLY A:55 , LYS A:56 , CYS A:77 , HIS A:78 , ALA A:79 , ILE A:100 , ASN A:138 , CYS A:139 , CYS A:142 , HIS A:143 , CYS A:181 , HIS A:185 , HEM A:802 , HEM A:803 , HEM A:805 , HOH A:884 , HOH A:1066BINDING SITE FOR RESIDUE HEM A 804
6AC6SOFTWARECYS A:139 , HIS A:143 , HIS A:171 , MET A:172 , CYS A:181 , CYS A:184 , HIS A:185 , GLY A:194 , ASN A:195 , MET A:197 , ASP A:205 , HIS A:206 , ILE A:207 , ASN A:399 , HIS A:400 , HEM A:802 , HEM A:804 , HOH A:849 , HOH A:901 , HOH A:951BINDING SITE FOR RESIDUE HEM A 805
7AC7SOFTWAREHIS A:171 , ASN A:177 , CYS A:184 , GLY A:208 , CYS A:209 , CYS A:212 , HIS A:213 , CYS A:232 , HIS A:236 , PRO A:404 , LYS A:405 , HOH A:887 , HOH A:965 , HOH A:1194BINDING SITE FOR RESIDUE HEM A 806
8AC8SOFTWAREHIS A:213 , PRO A:217 , HIS A:218 , THR A:227 , VAL A:230 , CYS A:232 , CYS A:235 , HIS A:236 , LYS A:405 , LEU A:409 , ASN A:410 , HEM A:808 , HOH A:966 , HOH A:1131 , HOH A:1142BINDING SITE FOR RESIDUE HEM A 807
9AC9SOFTWARELYS A:222 , LEU A:223 , HIS A:226 , ILE A:326 , LEU A:409 , ASN A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:423 , TYR A:428 , PRO A:432 , MET A:433 , HIS A:441 , HEM A:807 , HOH A:868BINDING SITE FOR RESIDUE HEM A 808

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SP3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SP3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SP3)

(-) Exons   (0, 0)

(no "Exon" information available for 1SP3)

(-) 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:436
 aligned with Q8E9W8_SHEON | Q8E9W8 from UniProtKB/TrEMBL  Length:461

    Alignment length:442
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458  
         Q8E9W8_SHEON    19 ANPHKDVLKGPFTTGSEVTTQCLTCHEEQATDMMKTSHWTWELEQKLPDRTVVRGKKNSINNFCVAISSNEPRCTSCHAGYGWKDNTFDFKDKTKVDCLICHDTTGTYVKDPAGAGEPMAKLDLAKIAQNVGAPVRDNCGSCHFYGGGGDAVKHGDLDSSMAYPDKATDVHMDSDGNNFQCQNCHTTEKHQISGNAMGVSPGGIDHIGCENCHDSAPHSNKKLNTHTATVACQTCHIPFFAKNEPTKMQWDWSTAGDDKPETVDQYGKHTYQKKKGNFVWEKMVKPQYAWYNGTANAYMAGDKMDSNVVTKLTYPMGDINDAKAKIYPFKVHTGKQIYDKKLNIFITPKTYGKGGYWSEFDWNLAAKLGMEANPTMLEKGIKYSGEYDFAATEMWWRINHMVSPKEQALNCNDCHNKGTRLDWQALGYQGDPMKNKQGPKHK 460
               SCOP domains d1sp3a_ A: Putative Cytochrome c                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------Cytochrome_C554-1sp3A01 A:21-144                                                                                            ------------------------------------------------------------------------------------------------------Cytochrome_cB-1sp3A02 A:247-420                                                                                                                                               ---------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.hhhhh..........hhhhhhhhh.............hhhhh.hhhhhh...................hhhhhhhh....hhhhhhhhhh..------.....hhhhhh................hhhhhh.ee..ee...........................hhhhhhhh...hhhhhhh........eeeeee.hhh...............ee...eeeeee.....eeeee...eee............ee.eee.........eeeeeeeeeeeeeee....ee.........hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee......hhhhh.hhhhhh........................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sp3 A   1 ANPHKDVLKGPFTTGSEVTTQCLTCHEEQATDMMKTSHWTWELEQKLPDRTVVRGKKNSINNFCVAISSNEPRCTSCHAGYGWKDNTFDFKDKTKVDCLICHDTTGTYVKDPAGAGEPMAKLDLAKIAQNVGAPVRDNCGSCHFYG------KHGDLDSSMAYPDKATDVHMDSDGNNFQCQNCHTTEKHQISGNAMGVSPGGIDHIGCENCHDSAPHSNKKLNTHTATVACQTCHIPFFAKNEPTKMQWDWSTAGDDKPETVDQYGKHTYQKKKGNFVWEKMVKPQYAWYNGTANAYMAGDKMDSNVVTKLTYPMGDINDAKAKIYPFKVHTGKQIYDKKLNIFITPKTYGKGGYWSEFDWNLAAKLGMEANPTMLEKGIKYSGEYDFAATEMWWRINHMVSPKEQALNCNDCHNKGTRLDWQALGYQGDPMKNKQGPKHK 442
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     |   -  |    160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440  
                                                                                                                                                                           146    153
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1SP3)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Multiheme_cytos (34)
(-)
Clan: no clan defined [family: Cytochrome_cB] (1)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8E9W8_SHEON | Q8E9W8)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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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