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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8 DIAMINOPELARGONIC ACID SYNTHASE APOENZYME IN BACILLUS SUBTILIS
 
Authors :  S. Dey, J. C. Sacchettini
Date :  11 Jul 08  (Deposition) - 23 Jun 09  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Biotin Biosynthesis, Pyridoxal Phosphate, S- Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Dey, J. M. Lane, R. E. Lee, E. J. Rubin, J. C. Sacchettini
Structural Characterization Of The Mycobacterium Tuberculosis Biotin Biosynthesis Enzymes 7, 8-Diaminopelargonic Acid Synthase And Dethiobiotin Synthetase .
Biochemistry V. 49 6746 2010
PubMed-ID: 20565114  |  Reference-DOI: 10.1021/BI902097J

(-) Compounds

Molecule 1 - ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BIOA
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
    Synonym: 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE, DAPA AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DRD)

(-) Sites  (0, 0)

(no "Site" information available for 3DRD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.BIOK_BACSU248-285
 		  2A:248-285
B:248-285

(-) Exons   (0, 0)

(no "Exon" information available for 3DRD)

(-) 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:419
 aligned with BIOK_BACSU | P53555 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
           BIOK_BACSU     1 MTHDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKNGYHGDTIGAVSVGSIELFHHVYGPLMFESYKAPIPYVYRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLED 448
               SCOP domains d3drda_ A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------3drdA02 A:62-338 Type I PLP-dependent aspartate aminotransferase-like (Major domai                             n)                                                                                                                                                                    -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....hhhhhhhh..eeeeee..eeee....eee..hhhhhh......hhhhhhhhhhhhh..........eehhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee-----------------------------.eeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeeee..ee.....ee...hhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh.....eeeeeehhhhhhhh.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee...........hhhhhhhhhhhhhhhhh.....ee..eeee......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:248-285   ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3drd A   1 MTHDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMK-----------------------------SYKAPIPYVYRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLED 448
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  |      -         -         -  |    180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
                                                                                                                                                                        143                           173                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:417
 aligned with BIOK_BACSU | P53555 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:446
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441      
           BIOK_BACSU     2 THDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKNGYHGDTIGAVSVGSIELFHHVYGPLMFESYKAPIPYVYRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLE 447
               SCOP domains d3drdb_ B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------3drdB02 B:62-338 Type I PLP-dependent aspartate aminotransferase-like (Major domai                             n)                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.....hhhhhhhh..eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........eehhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.-----------------------------.eee...hhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeeee..ee.....ee...hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeeehhhhhh...hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee..ee..eeee......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:248-285   ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3drd B   2 THDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSSVWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPKKLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMK-----------------------------SYKAPIPYVYRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPEGYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKGITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALENLALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRSKETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSEMVAIMKQAIHEVTSLE 447
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 |       -         -         - |     181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441      
                                                                                                                                                                       143                           173
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DRD)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BIOK_BACSU | P53555)
molecular function
    GO:0004015    adenosylmethionine-8-amino-7-oxononanoate transaminase activity    Catalysis of the reaction: 8-amino-7-oxononanoate + S-adenosyl-L-methionine(1+) = 7,8-diaminononanoate + S-adenosyl-4-methylthio-2-oxobutanoate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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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  3drd
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 Related Entries

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

UniProtKB/Swiss-Prot
        BIOK_BACSU | P53555: 3dod 3du4

(-) Related Entries Specified in the PDB File

3dod PLP-BOUND ENZYME