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(-) Description

Title :  CRITHIDIA FASCICULATA CYTOCHROME C
 
Authors :  V. Fulop, K. A. Sam, S. J. Ferguson, M. L. Ginger, J. W. A. Allen
Date :  25 May 11  (Deposition) - 15 Jun 11  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Electron Transport, Intermembrane Space, Metal-Binding, Thioether Bond, Respiratory Chain, Trypanosome, Mitochondrion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Fulop, K. A. Sam, S. J. Ferguson, M. L. Ginger, J. W. A. Allen
Structure Of A Trypanosomatid Mitochondrial Cytochrome C With Heme Attached Via Only One Thioether Bond And Implications For The Substrate Recognition Requirements Of Heme Lyase.
Febs J. V. 276 2822 2009
PubMed-ID: 19459937  |  Reference-DOI: 10.1111/J.1742-4658.2009.07005.X

(-) Compounds

Molecule 1 - CYTOCHROME C
    Chains: A, B, C
    Organism Scientific: CRITHIDIA FASCICULATA
    Organism Taxid: 5656
    Synonym: CYTOCHROME C555

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2M3L3Mod. Amino AcidN-TRIMETHYLLYSINE
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 26)
No.NameCountTypeFull Name
1HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2M3L6Mod. Amino AcidN-TRIMETHYLLYSINE
3SO414Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:24 , ALA A:25 , GLN A:27 , CYS A:28 , HIS A:29 , VAL A:39 , LEU A:46 , SER A:51 , GLY A:52 , ILE A:54 , TYR A:57 , TYR A:59 , SER A:60 , ASN A:63 , TRP A:70 , TYR A:78 , LEU A:79 , THR A:89 , LYS A:90 , MET A:91 , SER A:92 , HOH A:2121 , ASN B:37 , GLY B:38BINDING SITE FOR RESIDUE HEM A 200
02AC2SOFTWAREARG A:24 , GLY A:95 , MET A:96 , LYS A:97 , HOH A:2067 , HOH A:2178 , HOH A:2182 , HOH A:2197BINDING SITE FOR RESIDUE SO4 A1115
03AC3SOFTWAREARG A:49 , HOH A:2122 , HOH A:2198BINDING SITE FOR RESIDUE SO4 A1116
04AC4SOFTWARELYS A:90 , HOH A:2172 , HOH A:2199 , HOH A:2200 , HOH A:2201 , HOH A:2202 , HOH A:2203 , LYS B:90 , LYS C:90BINDING SITE FOR RESIDUE SO4 A1117
05AC5SOFTWAREARG B:24 , ALA B:25 , GLN B:27 , CYS B:28 , HIS B:29 , VAL B:39 , LEU B:46 , SER B:51 , GLY B:52 , ILE B:54 , TYR B:57 , TYR B:59 , SER B:60 , ASN B:63 , TRP B:70 , TYR B:78 , LEU B:79 , THR B:89 , LYS B:90 , MET B:91 , SER B:92 , HOH B:2120 , ASN C:37BINDING SITE FOR RESIDUE HEM B 200
06AC6SOFTWAREARG B:24 , GLY B:95 , MET B:96 , LYS B:97 , HOH B:2173 , HOH B:2174 , HOH B:2177 , HOH B:2189 , HOH B:2190BINDING SITE FOR RESIDUE SO4 B1115
07AC7SOFTWAREARG B:49 , HOH B:2121 , HOH B:2122BINDING SITE FOR RESIDUE SO4 B1116
08AC8SOFTWAREASN A:37 , ARG C:24 , ALA C:25 , GLN C:27 , CYS C:28 , HIS C:29 , VAL C:39 , LEU C:43 , LEU C:46 , SER C:51 , GLY C:52 , ILE C:54 , TYR C:57 , TYR C:59 , SER C:60 , ASN C:63 , TRP C:70 , TYR C:78 , LEU C:79 , THR C:89 , LYS C:90 , MET C:91 , SER C:92 , HOH C:2096BINDING SITE FOR RESIDUE HEM C 200
09AC9SOFTWAREARG C:24 , GLY C:95 , LYS C:97 , HOH C:2050 , HOH C:2150 , HOH C:2157 , HOH C:2170BINDING SITE FOR RESIDUE SO4 C1115
10BC1SOFTWAREARG C:49 , HOH C:2097 , HOH C:2103 , HOH C:2107BINDING SITE FOR RESIDUE SO4 C1116

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YK3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YK3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CYC_CRIFA_001 *E65DCYC_CRIFA  ---  ---A/B/CE65D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CYC_CRIFA_001 *E65DCYC_CRIFA  ---  ---A/B/CE65D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_CRIFA12-113
 
 		  3A:12-113
B:12-113
C:12-113
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_CRIFA12-113
 
 		  6A:12-113
B:12-113
C:12-113

(-) Exons   (0, 0)

(no "Exon" information available for 2YK3)

(-) 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:110
 aligned with CYC_CRIFA | P00078 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:110
                                    14        24        34        44        54        64        74        84        94       104       114
            CYC_CRIFA     5 ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTIEGYAYSKANAESGVVWTPDVLDVYLENPKKFMPGTKMSFAGMKKPQERADVIAYLETLKG 114
               SCOP domains d2yk3a_ A: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------D------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CYTC  PDB: A:12-113 UniProt: 12-113                                                                   - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2yk3 A   5 ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTIEGYAYSKANAESGVVWTPDVLDVYLENPkKFMPGTKMSFAGMKKPQERADVIAYLETLKG 114
                                    14        24        34        44        54        64        74        84        94       104       114
                                                                                                         83-M3L                           


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with CYC_CRIFA | P00078 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:110
                                    14        24        34        44        54        64        74        84        94       104       114
            CYC_CRIFA     5 ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTIEGYAYSKANAESGVVWTPDVLDVYLENPKKFMPGTKMSFAGMKKPQERADVIAYLETLKG 114
               SCOP domains d2yk3b_ B: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------D------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CYTC  PDB: B:12-113 UniProt: 12-113                                                                   - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2yk3 B   5 ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTIEGYAYSKANAESGVVWTPDVLDVYLENPkKFMPGTKMSFAGMKKPQERADVIAYLETLKG 114
                                    14        24        34        44        54        64        74        84        94       104       114
                                                                                                         83-M3L                           


Chain C from PDB  Type:PROTEIN  Length:110
 aligned with CYC_CRIFA | P00078 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:110
                                    14        24        34        44        54        64        74        84        94       104       114
            CYC_CRIFA     5 ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTIEGYAYSKANAESGVVWTPDVLDVYLENPKKFMPGTKMSFAGMKKPQERADVIAYLETLKG 114
               SCOP domains d2yk3c_ C: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Cytochrom_C-2yk3C01 C:14-113                                                                        - Pfam domains (1)
           Pfam domains (2) ---------Cytochrom_C-2yk3C02 C:14-113                                                                        - Pfam domains (2)
           Pfam domains (3) ---------Cytochrom_C-2yk3C03 C:14-113                                                                        - Pfam domains (3)
         Sec.struct. author ........hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------D------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CYTC  PDB: C:12-113 UniProt: 12-113                                                                   - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2yk3 C   5 ARAPLPPGDAARGEKLFKGRAAQCHTANQGGANGVGPNLYGLVGRHSGTIEGYAYSKANAESGVVWTPDVLDVYLENPkKFMPGTKMSFAGMKKPQERADVIAYLETLKG 114
                                    14        24        34        44        54        64        74        84        94       104       114
                                                                                                         83-M3L
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 3)

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

(-) CATH Domains  (0, 0 ; only for superseded entry 2W9K: 1,3)

(no "CATH Domain" information available for 2YK3, only for superseded entry 2W9K replaced by 2YK3)

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CYC_CRIFA | P00078)
molecular function
    GO:0009055    electron transfer 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: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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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