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(-) Description

Title :  NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
 
Authors :  P. M. Matias, R. Coelho, I. A. C. Pereira, A. V. Coelho, A. W. Thompson, L. Sieker, J. L. Gall, M. A. Carrondo
Date :  27 Nov 98  (Deposition) - 01 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transfer, Cytochrome, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. M. Matias, R. Coelho, I. A. Pereira, A. V. Coelho, A. W. Thompson, L. C. Sieker, J. L. Gall, M. A. Carrondo
The Primary And Three-Dimensional Structures Of A Nine-Haem Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774 Reveal A New Member Of The Hmc Family.
Structure Fold. Des. V. 7 119 1999
PubMed-ID: 10368280  |  Reference-DOI: 10.1016/S0969-2126(99)80019-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NINE-HAEM CYTOCHROME C)
    Atcc: 27774
    Cellular Location: PERIPLASMIC (PRESUMED)
    Chains: A, B
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2HEM18Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:11 , SER A:12 , HOH A:332 , HOH A:462BINDING SITE FOR RESIDUE ACT A 293
02AC2SOFTWARESER A:232 , PRO A:233 , HOH A:482 , HOH A:755 , ASP B:122 , GLU B:124 , HEM B:305BINDING SITE FOR RESIDUE ACT A 294
03AC3SOFTWAREHIS A:81 , TRP A:126 , HEM A:305BINDING SITE FOR RESIDUE ACT A 295
04AC4SOFTWAREASP A:122 , GLU A:124 , HEM A:305 , HOH A:634 , ARG B:231 , SER B:232 , PRO B:233BINDING SITE FOR RESIDUE ACT B 293
05AC5SOFTWAREMET B:260 , ALA B:261 , HIS B:264 , HOH B:511BINDING SITE FOR RESIDUE ACT B 294
06AC6SOFTWARESER A:8 , ALA A:10 , ILE A:14 , MET A:16 , PHE A:35 , HIS A:37 , ILE A:44 , CYS A:47 , CYS A:50 , HIS A:51 , PRO A:56 , VAL A:57 , SER A:58 , HEM A:303 , HOH A:382 , HOH A:432 , HOH A:519 , HOH A:538 , HOH A:583BINDING SITE FOR RESIDUE HEM A 301
07AC7SOFTWARECYS A:50 , HIS A:52 , THR A:53 , ASP A:55 , VAL A:57 , CYS A:59 , THR A:61 , CYS A:62 , HIS A:63 , GLU A:70 , GLY A:71 , ASP A:72 , ILE A:74 , ARG A:78 , ALA A:79 , MET A:80 , ARG A:88 , PRO A:94 , THR A:95 , HOH A:466 , HOH A:629 , HOH A:660BINDING SITE FOR RESIDUE HEM A 302
08AC8SOFTWAREVAL A:33 , PHE A:35 , ASN A:36 , ILE A:39 , HIS A:40 , LYS A:43 , THR A:95 , SER A:96 , CYS A:97 , CYS A:100 , HIS A:101 , LYS A:212 , LEU A:213 , ALA A:216 , HEM A:301 , HOH A:310 , HOH A:325 , HOH A:401 , HOH A:415 , HOH A:458 , HOH A:507 , HOH A:528BINDING SITE FOR RESIDUE HEM A 303
09AC9SOFTWAREGLN A:102 , THR A:105 , ARG A:108 , GLU A:110 , CYS A:111 , CYS A:114 , HIS A:115 , THR A:118 , THR A:119 , PRO A:120 , LYS A:121 , TRP A:126 , ILE A:208 , ASP A:211 , PHE A:217 , HIS A:218 , ILE A:223 , LEU A:224 , THR A:227 , HOH A:335 , HOH A:357BINDING SITE FOR RESIDUE HEM A 304
10BC1SOFTWAREMET A:16 , PHE A:17 , PRO A:18 , ALA A:29 , MET A:30 , LYS A:31 , PRO A:32 , 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 , ACT A:295 , HOH A:320 , HOH A:741 , ARG B:231 , PRO B:239 , SER B:243 , ACT B:293BINDING SITE FOR RESIDUE HEM A 305
11BC2SOFTWAREVAL A:172 , ALA 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 , SER A:235 , LEU A:236 , PRO A:238 , LYS A:240 , CYS A:241 , TYR A:263 , HEM A:308 , HOH A:314 , HOH A:481 , HOH A:750 , LYS B:26 , HOH B:375BINDING SITE FOR RESIDUE HEM A 306
12BC3SOFTWARECYS A:228 , HIS A:230 , ARG A:231 , LYS A:240 , CYS A:241 , CYS A:244 , HIS A:245 , ARG A:256 , PRO A:257 , ALA A:262 , LEU A:265 , GLU A:266 , HOH A:354 , HOH A:503 , HOH A:587 , HOH A:684BINDING SITE FOR RESIDUE HEM A 307
13BC4SOFTWARECYS A:114 , ILE A:117 , SER A:193 , PHE A:195 , THR A:196 , HIS A:200 , SER A:203 , LEU A:204 , CYS A:267 , CYS A:270 , HIS A:271 , MET A:274 , VAL A:276 , ARG A:278 , PRO A:279 , HEM A:306 , HEM A:309 , HOH A:392 , HOH A:426BINDING SITE FOR RESIDUE HEM A 308
14BC5SOFTWAREILE A:183 , ASP A:184 , ALA A:185 , LEU A:186 , ALA A:187 , ASP A:188 , LYS A:189 , TYR A:190 , SER A:193 , MET A:260 , TYR A:263 , HIS A:264 , CYS A:267 , MET A:268 , HIS A:271 , ARG A:280 , ASP A:281 , ASP A:283 , CYS A:284 , CYS A:287 , HIS A:288 , HEM A:308 , HOH A:322 , HOH A:352BINDING SITE FOR RESIDUE HEM A 309
15BC6SOFTWARESER 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 , CYS B:59 , HOH B:392 , HOH B:405 , HOH B:499BINDING SITE FOR RESIDUE HEM B 301
16BC7SOFTWARECYS 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 , THR B:95 , HOH B:447 , HOH B:508BINDING SITE FOR RESIDUE HEM B 302
17BC8SOFTWAREVAL B:33 , PHE B:35 , ASN B:36 , HIS B:40 , LYS B:43 , CYS B:50 , THR B:95 , CYS B:97 , CYS B:100 , HIS B:101 , LYS B:212 , LEU B:213 , ALA B:216 , HEM B:305 , HOH B:325 , HOH B:365 , HOH B:393 , HOH B:431 , HOH B:560 , HOH B:562 , HOH B:581BINDING SITE FOR RESIDUE HEM B 303
18BC9SOFTWAREGLN B:102 , THR B:105 , GLU B:110 , CYS B:111 , CYS B:114 , HIS B:115 , THR B:118 , THR B:119 , PRO B:120 , LYS B:121 , TRP B:126 , ILE B:208 , ASP B:211 , ALA B:214 , PHE B:217 , HIS B:218 , ILE B:223 , LEU B:224 , THR B:227 , HOH B:355 , HOH B:374 , HOH B:622BINDING SITE FOR RESIDUE HEM B 304
19CC1SOFTWAREARG A:231 , PRO A:239 , SER A:243 , ACT A:294 , MET B:16 , PHE B:17 , PRO B:18 , ALA B:29 , MET B:30 , PRO B:32 , VAL B:33 , LEU B:76 , MET B:80 , HIS B:81 , CYS B:97 , TRP B:126 , CYS B:127 , CYS B:130 , HIS B:131 , HEM B:303 , HOH B:321 , HOH B:332BINDING SITE FOR RESIDUE HEM B 305
20CC2SOFTWAREHOH A:747 , VAL B:172 , ALA B:177 , PRO B:178 , PHE B:195 , 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 , HEM B:308 , HOH B:333 , HOH B:342 , HOH B:394 , HOH B:615 , HOH B:623BINDING SITE FOR RESIDUE HEM B 306
21CC3SOFTWARECYS B:228 , HIS B:230 , ARG B:231 , LYS B:240 , CYS B:241 , CYS B:244 , HIS B:245 , GLY B:255 , ARG B:256 , PRO B:257 , ALA B:262 , LEU B:265 , GLU B:266 , HOH B:411 , HOH B:542 , HOH B:612BINDING SITE FOR RESIDUE HEM B 307
22CC4SOFTWARECYS B:114 , ILE B:183 , SER B:193 , PHE B:195 , THR B:196 , HIS B:200 , SER B:203 , LEU B:204 , GLU B:266 , CYS B:267 , CYS B:270 , HIS B:271 , MET B:274 , PRO B:279 , HEM B:306 , HOH B:639 , HOH B:648 , HOH B:694BINDING SITE FOR RESIDUE HEM B 308
23CC5SOFTWAREILE 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 , MET B:268 , HIS B:271 , ARG B:280 , ASP B:281 , CYS B:284 , CYS B:287 , HIS B:288 , HOH B:344 , HOH B:379BINDING SITE FOR RESIDUE HEM B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 19HC)

(-) 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 19HC)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC9_DESDA72-323
 		  2A:42-291
B:42-291

(-) Exons   (0, 0)

(no "Exon" information available for 19HC)

(-) 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:292
 aligned with CYC9_DESDA | Q9RN68 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:292
                                    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 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAP 322
               SCOP domains d19hca_ A: Nine-heme cytochrome c                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 19hcA02 A:1-99,A:130-167 Cytochrome C3                                                             19hcA01 A:100-129,A:168-292   19hcA02 A:1-99,A:130-167 Cytochrome C319hcA01 A:100-129,A:168-292 Cytochrome C3                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee................eeeehhhhhhh...hhhh........hhh.......hhh....hhhhhh...............hhhhhhhhhhh.hhhh.hhhh......hhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhh........hhh....eee.........eee.hhhhhhhhhhhh...hhhhhh.....hhhhh.............hhhh......hhh.....hhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------MULTIHEME_CYTC  PDB: A:42-291 UniProt: 72-323                                                                                                                                                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 19hc A   1 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIADCETCHHTGDPVSCSTCHTVEGKAEGDYITLDRAMHATDIAARAKGNTPTSCVSCHQSETKERRECAGCHAITTPKDDEAWCATCHDITPSMTPSEMQKGIAGTLLPGDNEALAAETVLAEATVAPVSPMLAPYKVVIDALADKYEPSDFTHRRHLTSLMESIKDDKLAQAFHDKPEILCATCHHRSPLSLTPPKCGSCHTKEIDAADPGRPNLMAAYHLECMGCHKGMAVARPRDTDCTTCHKAAA 292
                                    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:292
 aligned with CYC9_DESDA | Q9RN68 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:292
                                    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 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIDNCETCHHTGDPVSCSTCHTVEGKAEGNYITLDRAMHATNIAKRAKGNTPVSCVSCHEQQTKERRECAGCHAIVTPKRDEAWCATCHNITPSMTPEQMQKGINGTLLPGDNEALAAETVLAQKTVEPVSPMLAPYKVVIDALADKYEPSNFTHRRHLTSLMERIKDDKLAQAFHNKPEILCATCHHRSPLSLTPPKCGSCHTKEIDKANPGRPNLMAAYHLQCMGCHKGMDVARPRDTDCTTCHKAAP 322
               SCOP domains d19hcb_ B: Nine-heme cytochrome c                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 19hcB02 B:1-99,B:130-167 Cytochrome C3                                                             19hcB01 B:100-129,B:168-292   19hcB02 B:1-99,B:130-167 Cytochrome C319hcB01 B:100-129,B:168-292 Cytochrome C3                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee................eeeehhhhhhh...hhhh........hhh.......hhh....hhhhhh...............hhhhhhhhhhh.hhhh.hhh.......hhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhh........hhh....eee.........eee.hhhhhhhhhhhh...hhhhhh.....hhhhh.............hhhh......hhh.....hhhhhhhhhhhhhhh..........hhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------MULTIHEME_CYTC  PDB: B:42-291 UniProt: 72-323                                                                                                                                                                                                               PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 19hc B   1 AALEPTDSGAPSAIVMFPVGEKPNPKGAAMKPVVFNHLIHEKKIADCETCHHTGDPVSCSTCHTVEGKAEGDYITLDRAMHATDIAARAKGNTPTSCVSCHQSETKERRECAGCHAITTPKDDEAWCATCHDITPSMTPSEMQKGIAGTLLPGDNEALAAETVLAEATVAPVSPMLAPYKVVIDALADKYEPSDFTHRRHLTSLMESIKDDKLAQAFHDKPEILCATCHHRSPLSLTPPKCGSCHTKEIDAADPGRPNLMAAYHLECMGCHKGMAVARPRDTDCTTCHKAAA 292
                                    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)
1a19hcA02A:1-99,A:130-167
1b19hcB02B:1-99,B:130-167
1c19hcA01A:100-129,A:168-292
1d19hcB01B:100-129,B:168-292

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 19HC)

(-) 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: 1ofw 1ofy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 19HC)