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(-) Description

Title :  CRYSTAL STRUCTURE OF A DETHIOBIOTIN SYNTHETASE FROM FRANCISELLA TULARENSIS SUBSP. TULARENSIS SCHU S4
 
Authors :  J. S. Brunzelle, T. Skarina, E. Gordon, A. Savchenko, W. F. Anderson, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date :  13 Aug 10  (Deposition) - 02 Feb 11  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Dethiobiotin Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Brunzelle, T. Skarina, E. Gordon, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infections Diseases (Csgid)
Crystal Structure Of A Dethiobiotin Synthetase From Francisella Tularensis Subsp. Tularensis Schu S4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DETHIOBIOTIN SYNTHETASE
    Chains: A, B
    EC Number: 6.3.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BIOD, FTT_0934C
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 177416
    Strain: SCHU S4
    Synonym: DETHIOBIOTIN SYNTHASE, DTB SYNTHETASE, DTBS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3NA5Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:149 , CYS A:150 , ILE A:151 , ASN A:152 , HOH A:241 , ALA B:79 , HIS B:81 , THR B:121BINDING SITE FOR RESIDUE ACT A 500
2AC2SOFTWAREHIS A:126 , HOH A:290 , HOH A:339 , HOH A:429BINDING SITE FOR RESIDUE NA A 600
3AC3SOFTWAREASP A:102 , ASN A:105 , HOH A:325 , HOH A:366BINDING SITE FOR RESIDUE NA A 601
4AC4SOFTWARELYS A:37 , ALA A:40 , SER A:41 , ASP A:52 , ALA A:116 , HOH A:343 , HOH A:420 , HOH A:544BINDING SITE FOR RESIDUE ACT A 226
5AC5SOFTWAREALA A:79 , THR A:121 , GLY B:149 , CYS B:150 , ILE B:151 , ASN B:152 , HOH B:322BINDING SITE FOR RESIDUE ACT B 500
6AC6SOFTWAREASP B:102 , ASN B:105 , HOH B:357 , HOH B:467BINDING SITE FOR RESIDUE NA B 600
7AC7SOFTWAREASN B:162 , ASN B:165 , ASN B:179 , HOH B:337 , HOH B:360 , HOH B:437BINDING SITE FOR RESIDUE NA B 601
8AC8SOFTWAREHIS B:126 , HOH B:276 , HOH B:306 , HOH B:370 , HOH B:652BINDING SITE FOR RESIDUE NA B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OF5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OF5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OF5)

(-) Exons   (0, 0)

(no "Exon" information available for 3OF5)

(-) 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:222
 aligned with BIOD_FRATT | Q5NGB5 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:222
                               1                                                                                                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217  
           BIOD_FRATT     - ---MKKFFIIGTDTEVGKTYISTKLIEVCEHQNIKSLCLKPVASGQSQFSELCEDVESILNAYKHKFTAAEINLISFNQAVAPHIIAAKTKVDISIENLKQFIEDKYNQDLDILFIEGAGGLLTPYSDHTTQLDLIKALQIPVLLVSAIKVGCINHTLLTINELNRHNIKLAGWIANCNDSNIKYIDEQINTIEELSGYKCSAKISRNADYLDFIDLSKILI 219
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhhhhh...eeee..eee........hhhhhhhhhhh....hhhhhh.eee....hhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeeee.........hhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3of5 A  -2 SNAmKKFFIIGTDTEVGKTYISTKLIEVCEHQNIKSLCLKPVASGQSQFSELCEDVESILNAYKHKFTAAEINLISFNQAVAPHIIAAKTKVDISIENLKQFIEDKYNQDLDILFIEGAGGLLTPYSDHTTQLDLIKALQIPVLLVSAIKVGCINHTLLTINELNRHNIKLAGWIANCNDSNIKYIDEQINTIEELSGYKCSAKISRNADYLDFIDLSKILI 219
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217  
                               |                                                                                                                                                                                                                          
                               1-MSE                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with BIOD_FRATT | Q5NGB5 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                             1                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
           BIOD_FRATT     - -MKKFFIIGTDTEVGKTYISTKLIEVCEHQNIKSLCLKPVASGQSQFSELCEDVESILNAYKHKFTAAEINLISFNQAVAPHIIAAKTKVDISIENLKQFIEDKYNQDLDILFIEGAGGLLTPYSDHTTQLDLIKALQIPVLLVSAIKVGCINHTLLTINELNRHNIKLAGWIANCNDSNIKYIDEQINTIEELSGYKCSAKISRNADYLDFIDLSKILI 219
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --AAA_26-3of5B01 B:2-208                                                                                                                                                                                         ----------- Pfam domains (1)
           Pfam domains (2) --AAA_26-3of5B02 B:2-208                                                                                                                                                                                         ----------- Pfam domains (2)
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhhhhh...eeee..eee...---..hhhhhhhhhhh....hhhhhh.eee....hhhhhhhhhh...hhhhhhhhhhhhhhh...eeeee.......eee..eehhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3of5 B   0 AmKKFFIIGTDTEVGKTYISTKLIEVCEHQNIKSLCLKPVASGQS---ELCEDVESILNAYKHKFTAAEINLISFNQAVAPHIIAAKTKVDISIENLKQFIEDKYNQDLDILFIEGAGGLLTPYSDHTTQLDLIKALQIPVLLVSAIKVGCINHTLLTINELNRHNIKLAGWIANCNDSNIKYIDEQINTIEELSGYKCSAKISRNADYLDFIDLSKILI 219
                             |       9        19        29        39    |   49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
                             1-MSE                                     44  48
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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  (0, 0)

(no "SCOP Domain" information available for 3OF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OF5)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BIOD_FRATT | Q5NGB5)
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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