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(-) Description

Title :  STRUCTURE-BASED FUNCTIONAL IDENTIFICATION OF A NOVEL HEME-BINDING PROTEIN FROM THERMUS THERMOPHILUS HB8
 
Authors :  A. Ebihara, A. Okamoto, Y. Kousumi, H. Yamamoto, R. Masui, N. Ueyama, T. Shibata, Y. Inoue, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Mar 04  (Deposition) - 22 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Beta Barrel, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ebihara, A. Okamoto, Y. Kousumi, H. Yamamoto, R. Masui, N. Ueyama, S. Yokoyama, S. Kuramitsu
Structure-Based Functional Identification Of A Novel Heme-Binding Protein From Thermus Thermophilus Hb8.
J. Struct. Funct. Genom. V. 6 21 2005
PubMed-ID: 15965735  |  Reference-DOI: 10.1007/S10969-005-1103-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUCONOLACTONE ISOMERASE-LIKE PROTEIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VDH)

(-) Sites  (0, 0)

(no "Site" information available for 1VDH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VDH)

(-) 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:247
 aligned with Y1714_THET8 | Q5SHL6 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
          Y1714_THET8     3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGKVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
               SCOP domains d1vdha_ A: Polyketide synthase CurD homologue TTHA1714/TTC1352                                                                                                                                                                                          SCOP domains
               CATH domains 1vdhA01 A:3-123 Apc35880; domain 1                                                                                       1vdhA02 A:124-249 Apc35880; domain 2                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee...........hhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee........eeeeeee.hhhhhhhhhhhhh.hhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdh A   3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGEVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Y1714_THET8 | Q5SHL6 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
          Y1714_THET8     3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGKVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
               SCOP domains d1vdhb_ B: Polyketide synthase CurD homologue TTHA1714/TTC1352                                                                                                                                                                                          SCOP domains
               CATH domains 1vdhB01 B:3-123 Apc35880; domain 1                                                                                       1vdhB02 B:124-249 Apc35880; domain 2                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhh.hhhh.eeeeeeeeeeeeeee...........hhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee..hhhhhhhhhhhh.hhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdh B   3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGEVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       


Chain C from PDB  Type:PROTEIN  Length:247
 aligned with Y1714_THET8 | Q5SHL6 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
          Y1714_THET8     3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGKVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
               SCOP domains d1vdhc_ C: Polyketide synthase CurD homologue TTHA1714/TTC1352                                                                                                                                                                                          SCOP domains
               CATH domains 1vdhC01 C:3-123 Apc35880; domain 1                                                                                       1vdhC02 C:124-249 Apc35880; domain 2                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee...........hhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee..hhhhhhhhhhhh.hhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdh C   3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGEVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       


Chain D from PDB  Type:PROTEIN  Length:247
 aligned with Y1714_THET8 | Q5SHL6 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
          Y1714_THET8     3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGKVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
               SCOP domains d1vdhd_ D: Polyketide synthase CurD homologue TTHA1714/TTC1352                                                                                                                                                                                          SCOP domains
               CATH domains 1vdhD01 D:3-123 Apc35880; domain 1                                                                                       1vdhD02 D:124-249 Apc35880; domain 2                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee...........hhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee..hhhhhhhhhhhh.hhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdh D   3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGEVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       


Chain E from PDB  Type:PROTEIN  Length:247
 aligned with Y1714_THET8 | Q5SHL6 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:247
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       
          Y1714_THET8     3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGKVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
               SCOP domains d1vdhe_ E: Polyketide synthase CurD homologue TTHA1714/TTC1352                                                                                                                                                                                          SCOP domains
               CATH domains 1vdhE01 E:3-123 Apc35880; domain 1                                                                                       1vdhE02 E:124-249 Apc35880; domain 2                                                                                           CATH domains
           Pfam domains (1) --------------------------------Chlor_dismutase-1vdhE01 E:35-235                                                                                                                                                                         -------------- Pfam domains (1)
           Pfam domains (2) --------------------------------Chlor_dismutase-1vdhE02 E:35-235                                                                                                                                                                         -------------- Pfam domains (2)
           Pfam domains (3) --------------------------------Chlor_dismutase-1vdhE03 E:35-235                                                                                                                                                                         -------------- Pfam domains (3)
           Pfam domains (4) --------------------------------Chlor_dismutase-1vdhE04 E:35-235                                                                                                                                                                         -------------- Pfam domains (4)
           Pfam domains (5) --------------------------------Chlor_dismutase-1vdhE05 E:35-235                                                                                                                                                                         -------------- Pfam domains (5)
         Sec.struct. author .......eeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee...........hhhhhh.......eeeeeeeee.ee..ee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee..hhhhhhhhhhhh.hhhhhhheee...eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vdh E   3 RHVPEPTHTLEGWHVLHDFRLLDFARWFSAPLEAREDAWEELKGLVREWRELEEAGQGSYGIYQVVGHKADLLFLNLRPGLDPLLEAEARLSRSAFARYLGRSYSFYSVVELGSQEKPLDPESPYVKPRLTPRVPKSGYVCFYPMNKRRQGQDNWYMLPAKERASLMKAHGETGRKYQGEVMQVISGAQGLDDWEWGVDLFSEDPVQFKKIVYEMRFDEVSARYGEFGPFFVGKYLDEEALRAFLGL 249
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
   Legend:   → Mismatch (orange background)
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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, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 10)

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

(-) Pfam Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Clan: Dim_A_B_barrel (36)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Y1714_THET8 | Q5SHL6)
molecular function
    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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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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