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(-) Description

Title :  CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GTP
 
Authors :  M. M. Klimecka, P. J. Porebski, M. Chruszcz, K. Murzyn, A. Joachimiak, W Midwest Center For Structural Genomics (Mcsg)
Date :  01 Mar 11  (Deposition) - 30 Mar 11  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dtbs, Dethiobiotin Synthetase, Adp Binding, Structural Genomics, Psi- Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, , Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Porebski, M. Klimecka, M. Chruszcz, R. A. Nicholls, K. Murzyn, M. E. Cuff, X. Xu, M. Cymborowski, G. N. Murshudov, A. Savchenko, A. Edwards, W. Minor
Structural Characterization Of Helicobacter Pylori Dethiobiotin Synthetase Reveals Differences Between Family Members.
Febs J. V. 279 1093 2012
PubMed-ID: 22284390  |  Reference-DOI: 10.1111/J.1742-4658.2012.08506.X

(-) Compounds

Molecule 1 - DETHIOBIOTIN SYNTHETASE
    Chains: A
    EC Number: 6.3.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P11
    Expression System Strain: BL21 GOLD(DE3) MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: BIOD, HP0029, HP_0029
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: DTB SYNTHETASE, DTBS, DETHIOBIOTIN SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4NO31Ligand/IonNITRATE ION
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4NO32Ligand/IonNITRATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:9 , ASN A:10 , ALA A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , LYS A:35 , ASP A:50 , GLU A:116 , GLN A:167 , MG A:224 , EDO A:232 , HOH A:279 , HOH A:283 , HOH A:284 , HOH A:374 , HOH A:468 , HOH A:492 , HOH A:520BINDING SITE FOR RESIDUE GTP A 221
02AC2SOFTWAREASN A:42 , ASP A:43 , ARG A:74 , HIS A:76 , HOH A:364 , HOH A:451BINDING SITE FOR RESIDUE EDO A 222
03AC3SOFTWAREASN A:130 , ASP A:133 , HIS A:166 , HOH A:523BINDING SITE FOR RESIDUE EDO A 223
04AC4SOFTWARETHR A:14 , ASP A:50 , GLU A:116 , GTP A:221 , HOH A:374BINDING SITE FOR RESIDUE MG A 224
05AC5SOFTWAREASN A:25 , GLY A:28 , LYS A:30 , LEU A:61 , HOH A:310BINDING SITE FOR RESIDUE EDO A 225
06AC6SOFTWAREHIS A:0 , MET A:1 , LYS A:139 , LYS A:141 , SER A:220BINDING SITE FOR RESIDUE EDO A 226
07AC7SOFTWARELYS A:171 , THR A:181 , SER A:185 , VAL A:211 , HOH A:369 , HOH A:413 , HOH A:512BINDING SITE FOR RESIDUE EDO A 227
08AC8SOFTWARESER A:5 , ALA A:6 , LYS A:13 , GLY A:117 , ALA A:118 , GLY A:119 , GLY A:120 , LEU A:121 , MET A:131 , HOH A:391BINDING SITE FOR RESIDUE NO3 A 228
09AC9SOFTWARELEU A:168 , ASP A:169 , TYR A:170 , ASN A:200 , HOH A:493BINDING SITE FOR RESIDUE EDO A 229
10BC1SOFTWAREGLU A:87 , GLU A:88 , LEU A:217 , HOH A:448 , HOH A:481 , HOH A:484BINDING SITE FOR RESIDUE EDO A 230
11BC2SOFTWAREASN A:8 , ASN A:149BINDING SITE FOR RESIDUE EDO A 231
12BC3SOFTWARELYS A:35 , GLU A:38 , THR A:39 , ALA A:118 , GTP A:221 , HOH A:492 , HOH A:520BINDING SITE FOR RESIDUE EDO A 232

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QXJ)

(-) 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 BIOD_HELPY | O24872 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:224
                                1                                                                                                                                                                                                                      218  
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 |  
           BIOD_HELPY     - ----MLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALK--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----AAA_26-3qxjA01 A:1-208                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhh...eeee..ee..........hhhhhhhhhhh......hhhhhh.ee.....hhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxj A  -3 FQGHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALKGS 220
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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  (0, 0)

(no "SCOP Domain" information available for 3QXJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (BIOD_HELPY | O24872)
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.

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  3qxj
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  BIOD_HELPY | O24872
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  6.3.3.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        BIOD_HELPY | O24872: 2qmo 3mle 3qxc 3qxh 3qxs 3qxx 3qy0

(-) Related Entries Specified in the PDB File

2qmo CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI
3mle CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COCRYSTALLIZED WITH ATP
3qxc CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH ATP
3qxh CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH ADP AND 8-AMINOCAPRYLIC ACID
3qxs CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH ANP
3qxx CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GDP AND 8-AMINOCAPRYLIC ACID
3qy0 CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GDP