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(-) Description

Title :  DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 3-(1-AMINOETHYL) NONANEDIOIC ACID
 
Authors :  W. Huang, J. Jia, G. Schneider, Y. Lindqvist
Date :  08 May 95  (Deposition) - 20 Jun 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase, Biotin Biosynthesis, Magnesium, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Huang, J. Jia, K. J. Gibson, W. S. Taylor, A. R. Rendina, G. Schneider, Y. Lindqvist
Mechanism Of An Atp-Dependent Carboxylase, Dethiobiotin Synthetase, Based On Crystallographic Studies Of Complexes With Substrates And A Reaction Intermediate.
Biochemistry V. 34 10985 1995
PubMed-ID: 7669756  |  Reference-DOI: 10.1021/BI00035A004
(for further references see the PDB file header)

(-) Compounds

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

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1IKT1Ligand/Ion3-(1-AMINOETHYL)NONANEDIOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1IKT2Ligand/Ion3-(1-AMINOETHYL)NONANEDIOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:37 , ALA A:40 , SER A:41 , PRO A:79 , GLY A:150 , CYS A:151 , ILE A:152 , ASN A:153 , TYR A:187 , HOH A:342 , HOH A:343 , HOH A:360BINDING SITE FOR RESIDUE IKT A 225

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DAE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:219
 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 d1daea_ A: Dethiobiotin synthetase                                                                                                                                                                                               SCOP domains
               CATH domains 1daeA00 A:1-224 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhh....eeee..eee..eee..eee.hhhhhhhhh......hhhh..eee.....hhhhhhhh.....hhhhhhhhhhhhh...eeeee..............hhhhhhhh..eeeeeee....hhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhh....eeeee....-----...hhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dae A   1 SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLA-----AATGKYINLALL 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |  -  |    220    
                                                                                                                                                                                                                                        207   213
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  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 1DAE)

(-) 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

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

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

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