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(-) Description

Title :  THE Y66L MUTANT OF TETRAHEME CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS MIYAZAKI F
 
Authors :  Y. Higuchi, H. Komori
Date :  13 Jun 07  (Deposition) - 17 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Electron Transport, Heme, Iron, Metal-Binding, Periplasmic, Sulfate Respiration, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Takayama, H. Komori, K. Morita, Y. Higuchi, H. Akutsu
Structures Of Noncoordinated Aromatic Residue Mutants In Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris Miyazaki F
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C3
    ChainsA, B
    EngineeredYES
    Expression SystemSHEWANELLA
    Expression System Taxid22
    MutationYES
    Organism ScientificDESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'
    Organism Taxid883
    StrainMIYAZAKI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1HEM8Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:11 , ASP A:12 , LYS A:13 , THR A:14 , LYS A:15 , GLN A:16 , PRO A:17 , LYS A:57 , TYR A:65 , LEU A:66 , HIS A:70 , HIS A:83 , LEU A:97 , THR A:98 , GLY A:99 , CYS A:100 , CYS A:105 , HIS A:106BINDING SITE FOR RESIDUE HEM A 1004
2AC2SOFTWAREHIS A:35 , ASP A:42 , GLN A:44 , LYS A:45 , CYS A:46 , CYS A:51 , HIS A:52 , HIS A:67 , ALA A:68 , THR A:74 , LYS A:75 , PHE A:76 , HOH A:1034 , HOH A:1049 , HOH A:1087 , HOH A:1090 , HOH A:1091 , HOH A:1099BINDING SITE FOR RESIDUE HEM A 1002
3AC3SOFTWAREPRO A:2 , LYS A:3 , PRO A:5 , PHE A:20 , HIS A:22 , CYS A:30 , CYS A:33 , HIS A:34 , TYR A:43 , LYS A:45 , CYS A:46 , HOH A:1007 , HOH A:1020 , HOH A:1021BINDING SITE FOR RESIDUE HEM A 1001
4AC4SOFTWAREASN A:21 , THR A:24 , HIS A:25 , CYS A:79 , CYS A:82 , HIS A:83 , LYS A:93 , LYS A:104 , HOH A:1012 , HOH A:1064BINDING SITE FOR RESIDUE HEM A 1003
5AC5SOFTWAREMET B:2011 , ASP B:2012 , LYS B:2013 , THR B:2014 , LYS B:2015 , GLN B:2016 , PRO B:2017 , TYR B:2065 , HIS B:2070 , HIS B:2083 , LEU B:2097 , THR B:2098 , GLY B:2099 , CYS B:2100 , CYS B:2105 , HIS B:2106 , HOH B:3089BINDING SITE FOR RESIDUE HEM B 3004
6AC6SOFTWAREHIS B:2035 , ASP B:2042 , GLN B:2044 , CYS B:2046 , CYS B:2051 , HIS B:2052 , HIS B:2067 , ALA B:2068 , THR B:2074 , LYS B:2075 , PHE B:2076 , HOH B:3046 , HOH B:3054 , HOH B:3067 , HOH B:3074 , HOH B:3110BINDING SITE FOR RESIDUE HEM B 3002
7AC7SOFTWAREPRO B:2002 , LYS B:2003 , ALA B:2004 , PRO B:2005 , MET B:2011 , PHE B:2020 , HIS B:2022 , CYS B:2030 , CYS B:2033 , HIS B:2034 , TYR B:2043 , LYS B:2045 , CYS B:2046 , HOH B:3010 , HOH B:3052 , HOH B:3069 , HOH B:3128BINDING SITE FOR RESIDUE HEM B 3001
8AC8SOFTWAREASN B:2021 , THR B:2024 , HIS B:2025 , LYS B:2077 , CYS B:2079 , CYS B:2082 , HIS B:2083 , LYS B:2093 , LYS B:2104 , HOH B:3006 , HOH B:3044 , HOH B:3049 , HOH B:3068 , HOH B:3070BINDING SITE FOR RESIDUE HEM B 3003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z47)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z47)

(-) 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:107
 aligned with CYC3_DESVM | P00132 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:107
                                    33        43        53        63        73        83        93       103       113       123       
          CYC3_DESVM     24 APKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS  130
               SCOP domains d2z47a_ A: Cytochrome c3                                                                                    SCOP domains
               CATH domains 2z47A00 A:1-107 Cytochrome C3                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eeehhhhhh..hhhhhh.ee..ee......................hhhhhhhh......hhhhhhhhhhh.hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                2z47 A    1 APKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDYQKCATAGCHDNMDKKDKSAKGYLHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS  107
                                    10        20        30        40        50        60        70        80        90       100       

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with CYC3_DESVM | P00132 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:107
                                    33        43        53        63        73        83        93       103       113       123       
          CYC3_DESVM     24 APKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS  130
               SCOP domains d2z47b_ B: Cytochrome c3                                                                                    SCOP domains
               CATH domains 2z47B00 B:2001-2107 Cytochrome C3                                                                           CATH domains
           Pfam domains (1) Cytochrom_CIII-2z47B01 B:2001-2106                                                                        - Pfam domains (1)
           Pfam domains (2) Cytochrom_CIII-2z47B02 B:2001-2106                                                                        - Pfam domains (2)
         Sec.struct. author ........eee......eeehhhhhh..hhhhhh.ee..ee......................hhhhhhhh......hhhhhhhhhhh.hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                2z47 B 2001 APKAPADGLKMDKTKQPVVFNHSTHKAVKCGDCHHPVNGKEDYQKCATAGCHDNMDKKDKSAKGYLHAMHDKGTKFKSCVGCHLETAGADAAKKKELTGCKGSKCHS 2107
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100       

   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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYC3_DESVM | P00132)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    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.
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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC3_DESVM | P001321it1 1j0o 1j0p 1wr5 2cdv 2ewi 2ewk 2ewu 2ffn 2yxc 2yyw 2yyx

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