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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF THE REDUCED FORM OF NINE-HEME CYTOCHROME C AT PH 7.5
 
Authors :  I. Bento, V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, M. A. Carrondo
Date :  22 Apr 03  (Deposition) - 18 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multiheme Cytochrome C, Electron Transport, Electron Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Bento, V. H. Teixeira, A. M. Baptista, C. M. Soares, P. M. Matias, M. A. Carrondo
Redox-Bohr And Other Cooperativity Effects In The Nine-Heme Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774: Crystallographic And Modeling Studies
J. Biol. Chem. V. 278 36455 2003
PubMed-ID: 12750363  |  Reference-DOI: 10.1074/JBC.M301745200

(-) Compounds

Molecule 1 - NINE HEME CYTOCHROME C
    Atcc: 27774
    Chains: A, B
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876
    Synonym: 9HCC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3HEC18Ligand/IonHEME C

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:122 , GLU A:124 , HOH A:2263 , LYS B:121 , SER B:232 , PRO B:233BINDING SITE FOR RESIDUE ACT A1302
02AC2SOFTWARESER A:8 , ALA A:10 , ILE A:14 , PHE A:35 , HIS A:37 , CYS A:47 , CYS A:50 , HIS A:51 , PRO A:56 , SER A:58 , HEC A:1295 , HOH A:2011 , HOH A:2049 , HOH A:2243 , HOH A:2244 , HOH A:2245BINDING SITE FOR RESIDUE HEC A1293
03AC3SOFTWARECYS A:50 , HIS A:52 , THR A:53 , VAL A:57 , CYS A:59 , THR A:61 , CYS A:62 , HIS A:63 , GLU A:70 , GLY A:71 , ASN A:72 , ARG A:78 , ALA A:79 , MET A:80 , ARG A:88 , PRO A:94 , VAL A:95 , HOH A:2246BINDING SITE FOR RESIDUE HEC A1294
04AC4SOFTWAREVAL A:33 , PHE A:35 , ASN A:36 , ILE A:39 , HIS A:40 , LYS A:43 , VAL A:95 , SER A:96 , CYS A:97 , CYS A:100 , HIS A:101 , GLN A:104 , LYS A:212 , LEU A:213 , ALA A:216 , HEC A:1293 , HEC A:1297 , HOH A:2247 , HOH A:2248 , HOH A:2249 , HOH A:2250BINDING SITE FOR RESIDUE HEC A1295
05AC5SOFTWAREGLU A:102 , THR A:105 , ARG A:108 , GLU A:110 , CYS A:111 , CYS A:114 , HIS A:115 , VAL A:118 , PRO A:120 , LYS A:121 , TRP A:126 , ASP A:211 , PHE A:217 , HIS A:218 , ILE A:223 , THR A:227 , HOH A:2091 , HOH A:2105 , HOH A:2251 , HOH A:2252BINDING SITE FOR RESIDUE HEC A1296
06AC6SOFTWAREMET A:16 , PHE A:17 , PRO A:18 , ALA A:29 , MET A:30 , LYS A:31 , VAL A:33 , LEU A:76 , MET A:80 , HIS A:81 , CYS A:97 , TRP A:126 , CYS A:127 , CYS A:130 , HIS A:131 , HEC A:1295 , HOH A:2253 , HOH A:2254 , ARG B:231 , PRO B:239 , SER B:243BINDING SITE FOR RESIDUE HEC A1297
07AC7SOFTWAREALA A:177 , PRO A:178 , PHE A:195 , HIS A:197 , LEU A:201 , LEU A:224 , CYS A:225 , CYS A:228 , HIS A:229 , LEU A:236 , LYS A:240 , CYS A:241 , TYR A:263 , HEC A:1300 , HOH A:2256 , LYS B:26BINDING SITE FOR RESIDUE HEC A1298
08AC8SOFTWARECYS A:228 , HIS A:230 , ARG A:231 , LYS A:240 , CYS A:241 , CYS A:244 , HIS A:245 , GLY A:255 , ARG A:256 , PRO A:257 , ALA A:262 , LEU A:265 , GLN A:266 , HOH A:2103 , HOH A:2257 , GOL B:1302BINDING SITE FOR RESIDUE HEC A1299
09AC9SOFTWAREILE A:183 , SER A:193 , PHE A:195 , ARG A:199 , HIS A:200 , SER A:203 , LEU A:204 , ARG A:207 , GLN A:266 , CYS A:267 , CYS A:270 , HIS A:271 , MET A:274 , VAL A:276 , ARG A:278 , PRO A:279 , HEC A:1298 , HOH A:2258 , HOH A:2259 , HOH A:2260BINDING SITE FOR RESIDUE HEC A1300
10BC1SOFTWAREILE A:183 , ASP A:184 , ALA A:185 , LEU A:186 , ALA A:187 , ASP A:188 , LYS A:189 , TYR A:190 , TYR A:263 , HIS A:264 , MET A:268 , HIS A:271 , ASP A:281 , ASP A:283 , CYS A:284 , CYS A:287 , HIS A:288 , HOH A:2261 , HOH A:2262BINDING SITE FOR RESIDUE HEC A1301
11BC2SOFTWARESER B:8 , ALA B:10 , ILE B:14 , MET B:16 , PHE B:35 , HIS B:37 , ILE B:44 , CYS B:47 , CYS B:50 , HIS B:51 , PRO B:56 , SER B:58 , HEC B:1295 , HOH B:2222 , HOH B:2223BINDING SITE FOR RESIDUE HEC B1293
12BC3SOFTWARECYS B:50 , HIS B:52 , THR B:53 , VAL B:57 , CYS B:59 , THR B:61 , CYS B:62 , HIS B:63 , GLU B:70 , ARG B:78 , ALA B:79 , MET B:80 , ARG B:88 , PRO B:94 , VAL B:95 , HOH B:2094BINDING SITE FOR RESIDUE HEC B1294
13BC4SOFTWAREVAL B:33 , PHE B:35 , ASN B:36 , HIS B:40 , LYS B:43 , SER B:96 , CYS B:97 , CYS B:100 , HIS B:101 , GLN B:104 , LYS B:212 , LEU B:213 , ALA B:216 , HEC B:1293 , HOH B:2225 , HOH B:2226 , HOH B:2227 , HOH B:2228BINDING SITE FOR RESIDUE HEC B1295
14BC5SOFTWAREGLU B:102 , THR B:105 , ARG B:108 , GLU B:110 , CYS B:111 , CYS B:114 , HIS B:115 , LYS B:121 , TRP B:126 , ILE B:208 , ASP B:211 , PHE B:217 , HIS B:218 , ILE B:223 , THR B:227 , HOH B:2118 , HOH B:2229 , HOH B:2230BINDING SITE FOR RESIDUE HEC B1296
15BC6SOFTWAREARG A:231 , PRO A:239 , SER A:243 , GOL A:1303 , MET B:16 , PHE B:17 , PRO B:18 , ALA B:29 , MET B:30 , LYS B:31 , PRO B:32 , LEU B:76 , MET B:80 , HIS B:81 , CYS B:97 , TRP B:126 , CYS B:127 , CYS B:130 , HIS B:131 , GOL B:1302 , HOH B:2039 , HOH B:2042BINDING SITE FOR RESIDUE HEC B1297
16BC7SOFTWARELYS A:26 , HOH A:2019 , HOH A:2020 , ALA B:177 , PRO B:178 , HIS B:197 , LEU B:201 , LEU B:224 , CYS B:225 , CYS B:228 , HIS B:229 , LEU B:236 , LYS B:240 , CYS B:241 , TYR B:263 , HEC B:1300 , HOH B:2231 , HOH B:2232BINDING SITE FOR RESIDUE HEC B1298
17BC8SOFTWARECYS B:228 , HIS B:230 , ARG B:231 , LYS B:240 , CYS B:241 , CYS B:244 , HIS B:245 , PRO B:257 , ALA B:262 , LEU B:265 , GLN B:266 , HOH B:2233 , HOH B:2234 , HOH B:2235BINDING SITE FOR RESIDUE HEC B1299
18BC9SOFTWARECYS B:114 , ILE B:183 , SER B:193 , PHE B:195 , THR B:196 , ARG B:199 , HIS B:200 , SER B:203 , ARG B:207 , CYS B:267 , CYS B:270 , HIS B:271 , MET B:274 , VAL B:276 , PRO B:279 , HEC B:1298 , HOH B:2236 , HOH B:2237 , HOH B:2238 , HOH B:2239BINDING SITE FOR RESIDUE HEC B1300
19CC1SOFTWAREILE B:183 , ASP B:184 , ALA B:185 , LEU B:186 , ALA B:187 , ASP B:188 , LYS B:189 , TYR B:190 , MET B:260 , TYR B:263 , HIS B:264 , CYS B:267 , MET B:268 , ARG B:280 , CYS B:284 , CYS B:287 , HIS B:288 , HOH B:2240 , HOH B:2241BINDING SITE FOR RESIDUE HEC B1301
20CC2SOFTWARESER A:232 , PRO A:233 , HOH A:2192 , ARG B:122 , GLU B:124 , CYS B:127 , HEC B:1297 , HOH B:2117BINDING SITE FOR RESIDUE GOL A1303
21CC3SOFTWAREARG A:256 , HEC A:1299 , ASP B:77 , HIS B:81 , HEC B:1297 , HOH B:2091 , HOH B:2242BINDING SITE FOR RESIDUE GOL B1302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:278 -Pro A:279
2Arg B:278 -Pro B:279

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC9_DESDA72-323
 		  2A:42-293
B:42-293

(-) Exons   (0, 0)

(no "Exon" information available for 1OFY)

(-) 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:293
 aligned with CYC9_DESDA | Q9RN68 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:293
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   
           CYC9_DESDA    31 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 323
               SCOP domains d1ofya_ A: Nine-heme cytochrome c                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ofyA02 A:1-99,A:130-167 Cytochrome C3                                                             1ofyA01 A:100-129,A:168-292   1ofyA02 A:1-99,A:130-167 Cytochrome C31ofyA01 A:100-129,A:168-292 Cytochrome C3                                                                                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee................eeeehhhhhhhh.hhhhhh......hhhhh.....hhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhh...eee.........eeehhhhhhhhhhhh...hhhhhhhh...hhhhhhh...........hhhhhh............hhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------MULTIHEME_CYTC  PDB: A:42-293 UniProt: 72-323                                                                                                                                                                                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ofy A   1 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with CYC9_DESDA | Q9RN68 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:293
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   
           CYC9_DESDA    31 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 323
               SCOP domains d1ofyb_ B: Nine-heme cytochrome c                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ofyB02 B:1-99,B:130-167 Cytochrome C3                                                             1ofyB01 B:100-129,B:168-292   1ofyB02 B:1-99,B:130-167 Cytochrome C31ofyB01 B:100-129,B:168-292 Cytochrome C3                                                                                    - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofyB01 B:180-290                                                                               --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofyB02 B:180-290                                                                               --- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofyB03 B:180-290                                                                               --- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-1ofyB04 B:180-290                                                                               --- Pfam domains (4)
         Sec.struct. author .............eee................eeehhhhhhh...hhhhh.......hhhhh.....hhhhh..hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhh...eee.........eeehhhhhhhhhhhh...hhhhhhhh...hhhhhhh...........hhhhhh............hhhhhhhhhhhhhhhhh........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------MULTIHEME_CYTC  PDB: B:42-293 UniProt: 72-323                                                                                                                                                                                                                PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ofy B   1 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAPK 293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: Alpha-Beta Complex (3881)
(-)
Topology: Cytochrome C3 (62)
(-)
Homologous Superfamily: Cytochrome C3 (62)
(-)
Desulfovibrio desulfuricans. Organism_taxid: 876. (8)
1a1ofyA02A:1-99,A:130-167
1b1ofyA01A:100-129,A:168-292
1c1ofyB01B:100-129,B:168-292
1d1ofyB02B:1-99,B:130-167

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Multiheme_cytos (34)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CYC9_DESDA | Q9RN68)
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: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
        CYC9_DESDA | Q9RN68: 19hc 1ofw

(-) Related Entries Specified in the PDB File

19hc NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
1ofw REDOX-BOHR AND OTHER COOPERATIVITY EFFECTS IN THE NINE HEME CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774: CRYSTALLOGRAPHIC AND MODELING STUDIES.