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(-) Description

Title :  CRYSTAL STRUCTURE OF MOLYBDENUM COFACTOR BIOSYNTHESIS (AQ_061) FROM AQUIFEX AEOLICUS VF5
 
Authors :  J. Jeyakanthan, S. Mahesh, S. P. Kanaujia, S. Ramakumar, K. Sekar, Y. Ag A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken St Genomics/Proteomics Initiative (Rsgi)
Date :  29 Mar 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Molybdopterin, Mpt, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, S. Mahesh, S. P. Kanaujia, S. Ramakumar, K. Sekar, Y. Agari, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Molybdenum Cofactor Biosynthesis (Aq_061) From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MOLYBDENUM COFACTOR BIOSYNTHESIS MOG
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL-21 CONDON PLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2PBQ)

(-) Sites  (0, 0)

(no "Site" information available for 2PBQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PBQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PBQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PBQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PBQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PBQ)

(-) 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:174
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:174
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
         O66472_AQUAE     5 KAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
               SCOP domains d2pbqa_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeehhhhhh....hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pbq A   5 KAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:172
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
         O66472_AQUAE     4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFR 175
               SCOP domains d2pbqb_ B: a       utomated matches                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..-------.hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbq B   4 KKAVIGVVTISD-------EDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFR 175
                                    13 |      23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
                                      15      23                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:172
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:172
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
         O66472_AQUAE     4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFR 175
               SCOP domains d2pbqc_ C: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----MoCF_biosynth-2pbqC01 C:9-154                                                                                                                     --------------------- Pfam domains (1)
           Pfam domains (2) -----MoCF_biosynth-2pbqC02 C:9-154                                                                                                                     --------------------- Pfam domains (2)
           Pfam domains (3) -----MoCF_biosynth-2pbqC03 C:9-154                                                                                                                     --------------------- Pfam domains (3)
         Sec.struct. author ...eeeeeeehhhhhh....hhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbq C   4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFR 175
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PBQ)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MoCF_biosynth] (31)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (O66472_AQUAE | O66472)
biological process
    GO:0006777    Mo-molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
    GO:0032324    molybdopterin cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        O66472_AQUAE | O66472: 2qq1 3mci 3mcj

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