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(-) Description

Title :  STRUCTURE OF WILD-TYPE PHORMIDIUM LAMINOSUM CYTOCHROME C6
 
Authors :  J. A. R. Worrall, B. G. Schlarb-Ridley, T. Reda, M. J. Marcaida, R. J. Moorlen, J. Wastl, J. Hirst, D. S. Bendall, B. F. Luisi, C. J. Howe
Date :  10 May 07  (Deposition) - 24 Jul 07  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Cytochrome, Photosynthesis, Cyano-Bacteria, Electron-Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. R. Worrall, B. G. Schlarb-Ridley, T. Reda, M. J. Marcaida, R. J. Moorlen, J. Wastl, J. Hirst, D. S. Bendall, B. F. Luisi, C. J. Howe
Modulation Of Heme Redox Potential In The Cytochrome C(6) Family
J. Am. Chem. Soc. V. 129 9468 2007
PubMed-ID: 17625855  |  Reference-DOI: 10.1021/JA072346G

(-) Compounds

Molecule 1 - CYTOCHROME C6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPLC6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PHORMIDIUM LAMINOSUM
    Organism Taxid: 32059
    Other Details: ZN, IMIDAZOLE AND CHLORIDE IONS PRESENT IN THE STRUCTURE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD4Ligand/IonIMIDAZOLE
4ZN9Ligand/IonZINC ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD12Ligand/IonIMIDAZOLE
4ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:14 , CYS A:15 , CYS A:18 , HIS A:19 , ASN A:24 , VAL A:26 , ASN A:27 , LYS A:30 , THR A:31 , LEU A:32 , PHE A:40 , MET A:42 , GLN A:51 , VAL A:52 , LYS A:56 , ALA A:57 , GLY A:58 , MET A:59 , PRO A:60 , HOH A:2062 , HOH A:2063 , HOH A:2064 , ALA B:17BINDING SITE FOR RESIDUE HEM A1087
02AC2SOFTWAREASN A:24 , LEU A:25 , ALA A:28 , ZN A:1091 , HOH A:2018BINDING SITE FOR RESIDUE IMD A1088
03AC3SOFTWAREGLU A:35 , TYR A:77 , GLN A:81 , TRP A:86 , ZN A:1093 , CL A:1095 , CL A:1096 , CL A:1097BINDING SITE FOR RESIDUE IMD A1089
04AC4SOFTWAREASN B:14 , CYS B:15 , CYS B:18 , HIS B:19 , ASN B:24 , ASN B:27 , LYS B:30 , THR B:31 , LEU B:32 , PHE B:40 , MET B:42 , GLN B:51 , LYS B:56 , MET B:59 , PHE B:62 , HOH B:2039 , HOH B:2040BINDING SITE FOR RESIDUE HEM B1087
05AC5SOFTWAREASN B:24 , LEU B:25 , ZN B:1090 , HOH B:2013BINDING SITE FOR RESIDUE IMD B1088
06AC6SOFTWAREGLU B:35 , TYR B:77 , GLN B:81 , TRP B:86 , ZN B:1091BINDING SITE FOR RESIDUE IMD B1089
07AC7SOFTWAREASN A:27 , GLU A:29 , HOH A:2065 , HOH A:2066BINDING SITE FOR RESIDUE ZN A1090
08AC8SOFTWAREIMD A:1088 , HOH A:2067BINDING SITE FOR RESIDUE ZN A1091
09AC9SOFTWAREIMD B:1088 , HOH B:2041BINDING SITE FOR RESIDUE ZN B1090
10BC1SOFTWAREIMD B:1089 , HOH B:2042 , HOH B:2043 , HOH B:2044BINDING SITE FOR RESIDUE ZN B1091
11BC2SOFTWAREASP A:68 , HOH A:2068BINDING SITE FOR RESIDUE ZN A1092
12BC3SOFTWAREIMD A:1089 , CL A:1095 , CL A:1096 , CL A:1097BINDING SITE FOR RESIDUE ZN A1093
13BC4SOFTWAREASN B:27 , GLU B:29 , HOH B:2045 , HOH B:2046BINDING SITE FOR RESIDUE ZN B1092
14BC5SOFTWAREGLU B:35 , TRP B:86BINDING SITE FOR RESIDUE ZN B1093
15BC6SOFTWAREGLU A:35 , TRP A:86 , HOH A:2069BINDING SITE FOR RESIDUE ZN A1094
16BC7SOFTWAREGLY A:21 , THR A:31 , IMD A:1089 , ZN A:1093BINDING SITE FOR RESIDUE CL A1095
17BC8SOFTWAREPHE A:11 , GLY A:21 , IMD A:1089 , ZN A:1093 , CL A:1097 , HOH A:2030BINDING SITE FOR RESIDUE CL A1096
18BC9SOFTWAREGLU A:35 , ALA A:36 , LYS A:39 , IMD A:1089 , ZN A:1093 , CL A:1096BINDING SITE FOR RESIDUE CL A1097

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V08)

(-) Exons   (0, 0)

(no "Exon" information available for 2V08)

(-) 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:84
 aligned with CYC6_SYNLI | P00114 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
            CYC6_SYNLI    2 DLANGAKVFSGNCAACHMGGGNVVMANKTLKKEALEQFGMNSEDAIIYQVQHGKNAMPAFAGRLTDEQIQDVAAYVLDQAAKGW 85
               SCOP domains d2v08a_ A: automated matches                                                         SCOP domains
               CATH domains 2v08A00 A:3-86 Cytochrome c                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2v08 A  3 DLATGAKVFSANCAACHAGGINLVNAEKTLKKEALEKFGMNSIVAITTQVTNGKAGMPAFKGRLTDDQIAAVAAYVLDQAEKGW 86
                                    12        22        32        42        52        62        72        82    


Chain A from PDB  Type:PROTEIN  Length:84
 aligned with F2Z292_PHOLA | F2Z292 from UniProtKB/TrEMBL  Length:86

    Alignment length:84
                                    12        22        32        42        52        62        72        82    
          F2Z292_PHOLA    3 DLATGAKVFSANCAACHAGGINLVNAEKTLKKEALEKFGMNSIVAITTVVTNGKAGMPAFKGRLTDDQIAAVAAYVLDQAEKGW 86
               SCOP domains d2v08a_ A: automated matches                                                         SCOP domains
               CATH domains 2v08A00 A:3-86 Cytochrome c                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2v08 A  3 DLATGAKVFSANCAACHAGGINLVNAEKTLKKEALEKFGMNSIVAITTQVTNGKAGMPAFKGRLTDDQIAAVAAYVLDQAEKGW 86
                                    12        22        32        42        52        62        72        82    


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with CYC6_SYNLI | P00114 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:84
                                    11        21        31        41        51        61        71        81    
            CYC6_SYNLI    2 DLANGAKVFSGNCAACHMGGGNVVMANKTLKKEALEQFGMNSEDAIIYQVQHGKNAMPAFAGRLTDEQIQDVAAYVLDQAAKGW 85
               SCOP domains d2v08b_ B: automated matches                                                         SCOP domains
               CATH domains 2v08B00 B:3-86 Cytochrome c                                                          CATH domains
           Pfam domains (1) Cytochrome_CBB3-2v08B01 B:3-78                                              -------- Pfam domains (1)
           Pfam domains (2) Cytochrome_CBB3-2v08B02 B:3-78                                              -------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2v08 B  3 DLATGAKVFSANCAACHAGGINLVNAEKTLKKEALEKFGMNSIVAITTQVTNGKAGMPAFKGRLTDDQIAAVAAYVLDQAEKGW 86
                                    12        22        32        42        52        62        72        82    


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with F2Z292_PHOLA | F2Z292 from UniProtKB/TrEMBL  Length:86

    Alignment length:84
                                    12        22        32        42        52        62        72        82    
          F2Z292_PHOLA    3 DLATGAKVFSANCAACHAGGINLVNAEKTLKKEALEKFGMNSIVAITTVVTNGKAGMPAFKGRLTDDQIAAVAAYVLDQAEKGW 86
               SCOP domains d2v08b_ B: automated matches                                                         SCOP domains
               CATH domains 2v08B00 B:3-86 Cytochrome c                                                          CATH domains
           Pfam domains (1) Cytochrome_CBB3-2v08B01 B:3-78                                              -------- Pfam domains (1)
           Pfam domains (2) Cytochrome_CBB3-2v08B02 B:3-78                                              -------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2v08 B  3 DLATGAKVFSANCAACHAGGINLVNAEKTLKKEALEKFGMNSIVAITTQVTNGKAGMPAFKGRLTDDQIAAVAAYVLDQAEKGW 86
                                    12        22        32        42        52        62        72        82
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYC6_SYNLI | P00114)
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.
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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
cellular component
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0031977    thylakoid lumen    The volume enclosed by a thylakoid membrane.

Chain A,B   (F2Z292_PHOLA | F2Z292)
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.
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.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
cellular component
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0031977    thylakoid lumen    The volume enclosed by a thylakoid membrane.

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  2v08
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 Related Entries

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

UniProtKB/TrEMBL
        F2Z292_PHOLA | F2Z292: 3ph2

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