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(-) Description

Title :  CRYSTAL STRUCTURE OF MOLYBDENUM COFACTOR BIOSYNTHESIS (AQ_061) OTHER FORM FROM AQUIFEX AEOLICUS VF5
 
Authors :  J. Jeyakanthan, S. P. Kanaujia, K. Sekar, Y. Agari, A. Ebihara, S. Kuram A. Shinkai, S. Yokoyama, Riken Structural Genomics/Proteomics I (Rsgi)
Date :  29 Mar 10  (Deposition) - 19 Jan 11  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
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 :  S. P. Kanaujia, J. Jeyakanthan, A. Shinkai, S. Kuramitsu, S. Yokoyama K. Sekar
Crystal Structures, Dynamics And Functional Implications Of Molybdenum-Cofactor Biosynthesis Protein Moga From Two Thermophilic Organisms
Acta Crystallogr. , Sect. F V. 67 2 2011
PubMed-ID: 21206014  |  Reference-DOI: 10.1107/S1744309110035037

(-) Compounds

Molecule 1 - MOLYBDENUM COFACTOR BIOSYNTHESIS MOG
    Chains: A, B, C, D, E, F
    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
    Gene: MOG, AQ_061
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO E:135 , GLY E:136 , LYS E:137 , SER E:140 , HOH E:587BINDING SITE FOR RESIDUE EDO E 179

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MCJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MCJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MCJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MCJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3MCJ)

(-) Sequences/Alignments

Asymmetric 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
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    
         O66472_AQUAE     4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
               SCOP domains d3mcja_ A: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.........hhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhh..hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mcj A   4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173    


Chain B from PDB  Type:PROTEIN  Length:176
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      
         O66472_AQUAE     3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
               SCOP domains d3mcjb_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 3mcj B   3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      


Chain C from PDB  Type:PROTEIN  Length:173
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   
         O66472_AQUAE     4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRP 176
               SCOP domains d3mcjc_ C: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhh....hhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcj C   4 KKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRP 176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   


Chain D from PDB  Type:PROTEIN  Length:169
 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 d3mcjd_ D: au     tomated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...-----.hhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mcj D   5 KAVIGVVTISDRA-----EDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPKK 178
                                    14  |     24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174    
                                       17    23                                                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:166
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:173
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   
         O66472_AQUAE     5 KAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
               SCOP domains d3mcje_ E:        automated matches                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..-------..hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhh.eehhhhhhhhhhhhhh.hhhhhhh...eeee..eeeeee..hhhhhhhhhhhhh.hhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcj E   5 KAVIGVVTIS-------YEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
                                    14       |24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   
                                    14      22                                                                                                                                                           


Chain F from PDB  Type:PROTEIN  Length:175
 aligned with O66472_AQUAE | O66472 from UniProtKB/TrEMBL  Length:178

    Alignment length:175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
         O66472_AQUAE     3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
               SCOP domains d3mcjf_ F: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------MoCF_biosynth-3mcjF01 F:9-154                                                                                                                     ----------------------- Pfam domains (1)
           Pfam domains (2) ------MoCF_biosynth-3mcjF02 F:9-154                                                                                                                     ----------------------- Pfam domains (2)
           Pfam domains (3) ------MoCF_biosynth-3mcjF03 F:9-154                                                                                                                     ----------------------- Pfam domains (3)
           Pfam domains (4) ------MoCF_biosynth-3mcjF04 F:9-154                                                                                                                     ----------------------- Pfam domains (4)
           Pfam domains (5) ------MoCF_biosynth-3mcjF05 F:9-154                                                                                                                     ----------------------- Pfam domains (5)
           Pfam domains (6) ------MoCF_biosynth-3mcjF06 F:9-154                                                                                                                     ----------------------- Pfam domains (6)
         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
                 3mcj F   3 EKKAVIGVVTISDRASKGIYEDISGKAIIDYLKDVIITPFEVEYRVIPDERDLIEKTLIELADEKGCSLILTTGGTGPAPRDVTPEATEAVCEKMLPGFGELMRQVSLKQVPTAILSRQTAGIRGSCLIVNLPGKPQSIKVCLDAVMPAIPYCIDLIGGAYIDTDPNKVKAFRPK 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MCJ)

(-) Pfam Domains  (1, 6)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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

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

UniProtKB/TrEMBL
        O66472_AQUAE | O66472: 2pbq 2qq1 3mci

(-) Related Entries Specified in the PDB File

3mci