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(-) Description

Title :  MECHANISTIC IMPLICATIONS AND FAMILY RELATIONSHIPS FROM THE STRUCTURE OF DETHIOBIOTIN SYNTHETASE
 
Authors :  L. Sawyer, D. Alexeev
Date :  29 Nov 94  (Deposition) - 20 Apr 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Biotin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Alexeev, R. L. Baxter, L. Sawyer
Mechanistic Implications And Family Relationships From The Structure Of Dethiobiotin Synthetase.
Structure V. 2 1061 1994
PubMed-ID: 7881906  |  Reference-DOI: 10.1016/S0969-2126(94)00109-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DETHIOBIOTIN SYNTHETASE
    Chains: A
    EC Number: 6.3.3.3
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:12 , VAL A:13 , GLY A:14 , LYS A:15 , HOH A:401 , HOH A:402 , HOH A:446 , HOH A:466BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARELYS A:15 , LYS A:37 , ALA A:117 , GLY A:118 , HOH A:401 , HOH A:410 , HOH A:446 , HOH A:467BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARESER A:1 , ARG A:51 , GLN A:59 , TYR A:68 , HOH A:405 , HOH A:434 , HOH A:435 , HOH A:534 , HOH A:591 , HOH A:593BINDING SITE FOR RESIDUE SO4 A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DBS)

(-) 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:224
 aligned with BIOD1_ECOLI | P13000 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
          BIOD1_ECOLI     2 SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL 225
               SCOP domains d1dbsa_ A: Dethiobiotin synthetase                                                                                                                                                                                               SCOP domains
               CATH domains 1dbsA00 A:1-224 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhh...eeee.eeee...........hhhhhhhhh............eee.....hhhhhhhh.....hhhhhhhhhhhh....eeeeee.............hhhhhhhh...eeeee.....hhhhhhhhhhhhhhh......eeee........hhhhhhhhhhh.....eeee..................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dbs A   1 SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (BIOD1_ECOLI | P13000)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004141    dethiobiotin synthase activity    Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO(2) = ADP + dethiobiotin + 4 H(+) + phosphate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009102    biotin biosynthetic process    The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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UniProtKB/Swiss-Prot
        BIOD1_ECOLI | P13000: 1a82 1bs1 1byi 1dad 1dae 1daf 1dag 1dah 1dai 1dak 1dam 1dts

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