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(-) Description

Title :  HEXADECAHEME HIGH MOLECULAR WEIGHT CYTOCHROME HMC FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH
 
Authors :  M. Czjzek, R. Haser, M. Bruschi
Date :  25 Mar 02  (Deposition) - 13 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Electron Transport, Multiheme Cytochrome, Sulfate Reducing Bacteria, Periplasmic, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Czjzek, L. Elantak, V. Zamboni, X. Morelli, A. Dolla, F. Guerlesquin, M. Bruschi
The Crystal Structure Of The Hexadaca-Heme Cytochrome Hmc And A Structural Model Of Its Complex With Cytochrome C3
Structure V. 10 1677 2002
PubMed-ID: 12467575  |  Reference-DOI: 10.1016/S0969-2126(02)00909-7

(-) Compounds

Molecule 1 - HIGH-MOLECULAR-WEIGHT CYTOCHROME C
    ChainsA
    Organism ScientificDESULFOVIBRIO VULGARIS
    Organism Taxid882
    Other Details12 COVALENTLY LINKED HEMES
    StrainHILDENBOROUGH
    SynonymCYTOCHROME CC3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1HEC12Ligand/IonHEME C
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:33 , ARG A:34 , GLN A:37 , HIS A:38 , PHE A:64 , ASN A:82 , CYS A:83 , CYS A:86 , HIS A:87 , LEU A:90 , LYS A:96 , GLY A:98 , PRO A:99 , HOH A:2141BINDING SITE FOR RESIDUE HEM A 602
02AC2SOFTWAREGLY A:122 , PHE A:123 , HIS A:128 , HIS A:131 , ASN A:146 , CYS A:147 , CYS A:150 , HIS A:151 , GLU A:168 , SER A:170 , ARG A:172 , LEU A:234 , ARG A:236 , ASP A:276 , CYS A:277 , ARG A:278 , ILE A:285 , HEC A:606BINDING SITE FOR RESIDUE HEM A 604
03AC3SOFTWAREHIS A:35 , TRP A:118 , GLU A:120 , ILE A:121 , ARG A:172 , LEU A:186 , ALA A:190 , HIS A:191 , HIS A:198 , PRO A:210 , VAL A:211 , ASN A:212 , CYS A:213 , CYS A:216 , HIS A:217 , HEC A:601BINDING SITE FOR RESIDUE HEM A 607
04AC4SOFTWAREGLN A:238 , PHE A:265 , HIS A:267 , ALA A:274 , ASP A:276 , CYS A:277 , CYS A:280 , HIS A:281 , ILE A:285 , ASP A:286 , THR A:287 , CYS A:288 , HEC A:610 , HOH A:2146 , HOH A:2147BINDING SITE FOR RESIDUE HEM A 608
05AC5SOFTWAREPHE A:33 , HIS A:35 , CYS A:49 , CYS A:52 , HIS A:53 , LEU A:62 , LYS A:63 , PHE A:64 , ARG A:66 , TYR A:79 , HIS A:191 , HEM A:607 , HOH A:2140BINDING SITE FOR RESIDUE HEC A 601
06AC6SOFTWAREILE A:17 , GLY A:18 , ALA A:19 , MET A:20 , LEU A:26 , ASP A:27 , LEU A:28 , TYR A:79 , HIS A:80 , GLN A:100 , ASP A:101 , CYS A:104 , CYS A:107 , HIS A:108BINDING SITE FOR RESIDUE HEC A 603
07AC7SOFTWARELYS A:59 , HIS A:152 , TYR A:154 , SER A:170 , CYS A:171 , CYS A:174 , HIS A:175 , LYS A:182 , ALA A:193 , HOH A:2142BINDING SITE FOR RESIDUE HEC A 605
08AC8SOFTWAREPHE A:123 , ARG A:130 , HIS A:131 , CYS A:150 , CYS A:194 , CYS A:197 , HIS A:198 , GLU A:207 , THR A:208 , GLY A:209 , PRO A:210 , PHE A:225 , HEM A:604 , HOH A:2143 , HOH A:2144BINDING SITE FOR RESIDUE HEC A 606
09AC9SOFTWARECYS A:280 , HIS A:282 , ARG A:284 , THR A:287 , CYS A:288 , CYS A:291 , HIS A:292 , ASP A:299 , SER A:300 , LYS A:301 , ALA A:308 , GLN A:311 , SER A:314 , ARG A:316BINDING SITE FOR RESIDUE HEC A 609
10BC1SOFTWAREPHE A:265 , ASP A:266 , HIS A:270 , LYS A:273 , MET A:315 , ARG A:316 , SER A:317 , CYS A:318 , CYS A:321 , HIS A:322 , ARG A:386 , LYS A:433 , LEU A:434 , THR A:437 , HEM A:608 , HEC A:612 , HOH A:2071BINDING SITE FOR RESIDUE HEC A 610
11BC2SOFTWARECYS A:331 , CYS A:334 , HIS A:335 , PRO A:340 , THR A:341 , GLN A:346 , ASP A:432 , PHE A:438 , HIS A:439 , THR A:444 , LEU A:445 , GLN A:447 , HOH A:2149 , HOH A:2151BINDING SITE FOR RESIDUE HEC A 611
12BC3SOFTWAREGLU A:230 , ILE A:244 , LEU A:245 , PRO A:246 , THR A:259 , MET A:260 , LYS A:261 , PRO A:262 , VAL A:263 , LEU A:305 , GLU A:306 , MET A:309 , HIS A:310 , CYS A:347 , CYS A:350 , HIS A:351 , HEC A:610BINDING SITE FOR RESIDUE HEC A 612
13BC4SOFTWAREILE A:398 , PHE A:416 , HIS A:418 , VAL A:422 , CYS A:446 , CYS A:449 , HIS A:450 , SER A:456 , LEU A:457 , PRO A:459 , LYS A:461 , CYS A:462 , TYR A:484 , HEC A:615 , HOH A:2131BINDING SITE FOR RESIDUE HEC A 613
14BC5SOFTWAREPHE A:337 , LYS A:339 , CYS A:449 , HIS A:451 , ASN A:452 , CYS A:462 , SER A:464 , CYS A:465 , HIS A:466 , ARG A:477 , PRO A:478 , ALA A:483 , GLN A:486 , GLN A:487BINDING SITE FOR RESIDUE HEC A 614
15BC6SOFTWAREILE A:404 , SER A:414 , PHE A:416 , LYS A:420 , ILE A:421 , GLN A:487 , CYS A:488 , CYS A:491 , HIS A:492 , PRO A:500 , HEC A:613BINDING SITE FOR RESIDUE HEC A 615
16BC7SOFTWARETHR A:88 , GLN A:100 , ILE A:404 , GLY A:405 , SER A:406 , ILE A:407 , ALA A:408 , LYS A:409 , GLU A:410 , TYR A:411 , LYS A:481 , TYR A:484 , HIS A:485 , CYS A:488 , ASN A:502 , CYS A:505 , CYS A:508 , HIS A:509BINDING SITE FOR RESIDUE HEC A 616

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:499 -Pro A:500

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.HMWC_DESVH75-545  1A:44-512

(-) Exons   (0, 0)

(no "Exon" information available for 1GWS)

(-) 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:503
 aligned with HMWC_DESVH | P24092 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:503
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540   
           HMWC_DESVH    41 KRADLIEIGAMERFGKLDLPKVAFRHDQHTTAVTGMGKDCAACHKSKDGKMSLKFMRLDDNSAAELKEIYHANCIGCHTDLAKAGKKTGPQDGECRSCHNPKPSAASSWKEIGFDKSLHYRHVASKAIKPVGDPQKNCGACHHVYDEASKKLVWGKNKEDSCRACHGEKPVDKRPALDTAAHTACISCHMDVAKTKAETGPVNCAGCHAPEAQAKFKVVREVPRLDRGQPDAALILPVPGKDAPREMKGTMKPVAFDHKAHEAKANDCRTCHHVRIDTCTACHTVNGTADSKFVQLEKAMHQPDSMRSCVGCHNTRVQQPTCAGCHGFIKPTKSDAQCGVCHVAAPGFDAKQVEAGALLNLKAEQRSQVAASMLSARPQPKGTFDLNDIPEKVVIGSIAKEYQPSEFPHRKIVKTLIAGIGEDKLAATFHIEKGTLCQGCHHNSPASLTPPKCASCHGKPFDADRGDRPGLKAAYHQQCMGCHDRMKIEKPANTACVDCHKER 543
               SCOP domains d1gwsa_ A: 16-heme cytochrome c HmcA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1gwsA01 A:10-110 Cytochrome C3                                                                       -------1gwsA02 A:118-226 Cytochrome C3                                                                              -------------1gwsA03 A:240-314,A:350-388 Cytochrome C3                                  1gwsA04 A:315-349,A:389-512        1gwsA03 A:240-314,A:350-388            1gwsA04 A:315-349,A:389-512 Cytochrome C3                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeehhhhhhh......eeeehhhhhhhhhh...hhhhh..ee..ee..........hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh...............hhhhhhhhhh............hhhhh..eee....eee.......hhhhh..........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...............eeee..................eeeehhhhhhhh.............................hhhhhhhh.....hhhhhhhhhh.hhhhhhhhh......hhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhh...eee.........eeehhhhhhhhhhhhhh.hhhhhhhh....hhhhhh...........hhhhhh............hhhhhhhhhhhhhhhhh........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------MULTIHEME_CYTC  PDB: A:44-512 UniProt: 75-545                                                                                                                                                                                                                                                                                                                                                                                                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gws A  10 KRADLIEIGAMERFGKLDLPKVAFRHDQHTTAVTGMGKDCAACHKSKDGKMSLKFMRLDDNSAAELKEIYHANCIGCHTDLAKAGKKTGPQDGECRSCHNPKPSAASSWKEIGFDKSLHYRHVASKAIKPVGDPQKNCGACHHVYDEASKKLVWGKNKEDSCRACHGEKPVDKRPALDTAAHTACISCHMDVAKTKAETGPVNCAGCHAPEAQAKFKVVREVPRLDRGQPDAALILPVPGKDAPREMKGTMKPVAFDHKAHEAKANDCRTCHHVRIDTCTACHTVNGTADSKFVQLEKAMHQPDSMRSCVGCHNTRVQQPTCAGCHGFIKPTKSDAQCGVCHVAAPGFDAKQVEAGALLNLKAEQRSQVAASMLSARPQPKGTFDLNDIPEKVVIGSIAKEYQPSEFPHRKIVKTLIAGIGEDKLAATFHIEKGTLCQGCHHNSPASLTPPKCASCHGKPFDADRGDRPGLKAAYHQQCMGCHDRMKIEKPANTACVDCHKER 512
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GWS)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HMWC_DESVH | P24092)
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
        HMWC_DESVH | P240921h29 2cvc

(-) Related Entries Specified in the PDB File

1h29 SULFATE RESPIRATION IN DESULFOVIBRIO VULGARIS HILDENBOROUGH: STRUCTURE OF THE 16-HEME CYTOCHROME C HMCA AT 2.5 A RESOLUTION AND A VIEW OF ITS ROLE IN TRANSMEMBRANE ELECTRON TRANSFER