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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYTOCHROME C-552 FROM HYDROGENOBACTER THERMOPHILUS AT 2.0 RESOLUTION
 
Authors :  C. Travaglini-Allocatelli, S. Gianni, V. K. Dubey, A. Borgia, A. Di Ma D. Bonivento, F. Cutruzzola, K. L. Bren, M. Brunori
Date :  25 Jan 05  (Deposition) - 17 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Helix, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Travaglini-Allocatelli, S. Gianni, V. K. Dubey, A. Borgia, A. Di Matteo, D. Bonivento, F. Cutruzzola, K. L. Bren, M. Brunori
An Obligatory Intermediate In The Folding Pathway Of Cytochrome C552 From Hydrogenobacter Thermophilus
J. Biol. Chem. V. 280 25729 2005
PubMed-ID: 15883159  |  Reference-DOI: 10.1074/JBC.M502628200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C-552
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET17B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: HYDROGENOBACTER THERMOPHILUS
    Organism Taxid: 940

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1HEC4Ligand/IonHEME C
2MPD8Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:7 , LYS A:8 , HOH A:621 , HOH A:643 , LYS B:6 , LYS C:20BINDING SITE FOR RESIDUE SO4 A 502
02AC2SOFTWARELYS B:47 , THR B:65 , ASP B:66 , HOH B:612 , LYS C:19BINDING SITE FOR RESIDUE SO4 B 501
03AC3SOFTWARELYS A:20 , GLN C:7 , LYS C:8 , HOH C:636 , HOH C:638 , HOH C:661 , LYS D:6BINDING SITE FOR RESIDUE SO4 C 503
04AC4SOFTWARECYS A:10 , CYS A:13 , HIS A:14 , VAL A:21 , GLY A:22 , PRO A:23 , TYR A:32 , TYR A:41 , LYS A:45 , ILE A:46 , GLY A:50 , SER A:51 , GLY A:52 , VAL A:53 , TRP A:54 , GLY A:55 , VAL A:57 , MET A:59 , HOH A:610 , HOH A:633BINDING SITE FOR RESIDUE HEC A 81
05AC5SOFTWARECYS B:10 , CYS B:13 , HIS B:14 , GLY B:22 , PRO B:23 , TYR B:25 , TYR B:32 , TYR B:41 , LYS B:45 , ILE B:46 , GLY B:50 , SER B:51 , GLY B:52 , VAL B:53 , TRP B:54 , GLY B:55 , VAL B:57 , MET B:59 , HOH B:609 , HOH B:610BINDING SITE FOR RESIDUE HEC B 81
06AC6SOFTWAREMPD B:602 , CYS C:10 , CYS C:13 , HIS C:14 , VAL C:21 , GLY C:22 , PRO C:23 , TYR C:32 , TYR C:41 , LEU C:42 , LYS C:45 , ILE C:46 , GLY C:50 , SER C:51 , GLY C:52 , VAL C:53 , TRP C:54 , GLY C:55 , VAL C:57 , MET C:59 , HOH C:612 , HOH D:641BINDING SITE FOR RESIDUE HEC C 81
07AC7SOFTWARECYS D:10 , CYS D:13 , HIS D:14 , GLY D:22 , PRO D:23 , TYR D:25 , TYR D:32 , TYR D:41 , LYS D:45 , ILE D:46 , GLY D:50 , SER D:51 , GLY D:52 , VAL D:53 , TRP D:54 , GLY D:55 , VAL D:57 , MET D:59 , GLN D:62 , VAL D:64 , HOH D:606 , HOH D:612BINDING SITE FOR RESIDUE HEC D 81
08AC8SOFTWARELYS A:19 , LYS A:20 , VAL A:21 , GLY A:22 , HOH A:617 , HOH A:640 , HOH A:642BINDING SITE FOR RESIDUE MPD A 601
09AC9SOFTWAREALA A:12 , HOH A:620 , HOH A:634 , ASN C:63 , HOH C:613 , GLY D:9 , ALA D:12BINDING SITE FOR RESIDUE MPD A 603
10BC1SOFTWARETYR A:32 , ARG A:35 , ASP A:37BINDING SITE FOR RESIDUE MPD A 606
11BC2SOFTWAREHOH A:611 , HOH A:624 , ALA B:12 , ALA C:12 , CYS C:13 , HEC C:81BINDING SITE FOR RESIDUE MPD B 602
12BC3SOFTWARETYR B:32 , ARG B:35 , LYS B:36 , ALA B:38 , TYR B:41BINDING SITE FOR RESIDUE MPD B 607
13BC4SOFTWAREASN B:63 , HOH B:645 , LYS C:20 , HOH C:652BINDING SITE FOR RESIDUE MPD C 604
14BC5SOFTWAREARG C:35 , TYR C:41BINDING SITE FOR RESIDUE MPD C 608
15BC6SOFTWARELYS D:36BINDING SITE FOR RESIDUE MPD D 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YNR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YNR)

(-) Exons   (0, 0)

(no "Exon" information available for 1YNR)

(-) 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:80
 aligned with CY552_HYDTT | P15452 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:80
                                    28        38        48        58        68        78        88        98
           CY552_HYDTT   19 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 98
               SCOP domains d1ynra_ A: Cytochrome c552                                                       SCOP domains
               CATH domains 1ynrA00 A:1-80 Cytochrome c                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  1ynr A  1 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 80
                                    10        20        30        40        50        60        70        80


Chain B from PDB  Type:PROTEIN  Length:79
 aligned with CY552_HYDTT | P15452 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:79
                                    28        38        48        58        68        78        88         
           CY552_HYDTT   19 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSI 97
               SCOP domains d1ynrb_ B: Cytochrome c552                                                      SCOP domains
               CATH domains 1ynrB00 B:1-79 Cytochrome c                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                  1ynr B  1 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSI 79
                                    10        20        30        40        50        60        70         


Chain C from PDB  Type:PROTEIN  Length:80
 aligned with CY552_HYDTT | P15452 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:80
                                    28        38        48        58        68        78        88        98
           CY552_HYDTT   19 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 98
               SCOP domains d1ynrc_ C: Cytochrome c552                                                       SCOP domains
               CATH domains 1ynrC00 C:1-80 Cytochrome c                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  1ynr C  1 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSIK 80
                                    10        20        30        40        50        60        70        80


Chain D from PDB  Type:PROTEIN  Length:79
 aligned with CY552_HYDTT | P15452 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:79
                                    28        38        48        58        68        78        88         
           CY552_HYDTT   19 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSI 97
               SCOP domains d1ynrd_ D: Cytochrome c552                                                      SCOP domains
               CATH domains 1ynrD00 D:1-79 Cytochrome c                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                  1ynr D  1 NEQLAKQKGCMACHDLKAKKVGPAYADVAKKYAGRKDAVDYLAGKIKKGGSGVWGSVPMPPQNVTDAEAKQLAQWILSI 79
                                    10        20        30        40        50        60        70
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CY552_HYDTT | P15452)
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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CY552_HYDTT | P15452: 1ayg 2ai5 3vym 4zid 5aur 5aus

(-) Related Entries Specified in the PDB File

1ayg STRUCTURE OF THE CYTOCHROME C-552 FROM HYDROGENOBACTER THERMOPHILUS SOLVED BY NMR