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(-) Description

Title :  CRYSTAL STRUCTURE OF BACD, AN L-AMINO ACID DIPEPTIDE LIGASE FROM BACILLUS SUBTILIS
 
Authors :  Y. Shomura, Y. Higuchi
Date :  14 Dec 11  (Deposition) - 11 Apr 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Grasp Domain, Amino Acid Ligase, Atp Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shomura, E. Hinokuchi, H. Ikeda, A. Senoo, Y. Takahashi, J. Saito, H. Komori, N. Shibata, Y. Yonetani, Y. Higuchi
Structural And Enzymatic Characterization Of Bacd, An L-Amino Acid Dipeptide Ligase From Bacillus Subtilis
Protein Sci. 2012
PubMed-ID: 22407814  |  Reference-DOI: 10.1002/PRO.2058

(-) Compounds

Molecule 1 - ALANINE-ANTICAPSIN LIGASE BACD
    Chains: A
    EC Number: 6.3.2.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BACD, BSU37710, IPA-83D
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: BACILYSIN SYNTHETASE, L-AMINO ACID LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3P0D1Ligand/Ion(2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY)PHOSPHORYL]-2-BENZYLPROPANOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:311 , GLU A:324 , ADP A:503 , P0D A:504 , HOH A:719BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLU A:109 , LYS A:138 , LEU A:182 , ALA A:183 , GLU A:324 , ADP A:503 , P0D A:504 , HOH A:721BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWARELYS A:138 , ILE A:176 , LYS A:178 , LEU A:182 , ALA A:183 , SER A:184 , SER A:185 , VAL A:188 , GLU A:226 , GLU A:227 , PHE A:228 , LEU A:229 , GLN A:268 , PHE A:271 , GLU A:311 , ILE A:323 , GLU A:324 , MG A:501 , MG A:502 , P0D A:504 , HOH A:631 , HOH A:685 , HOH A:706 , HOH A:719BINDING SITE FOR RESIDUE ADP A 503
4AC4SOFTWARELEU A:12 , GLY A:13 , GLY A:14 , ALA A:183 , SER A:184 , GLU A:273 , HIS A:309 , GLU A:311 , GLU A:324 , ARG A:328 , GLY A:331 , MG A:501 , MG A:502 , ADP A:503 , HOH A:650 , HOH A:719 , HOH A:721 , HOH A:744 , HOH A:745BINDING SITE FOR RESIDUE P0D A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:173 -Pro A:174
2Thr A:278 -Pro A:279

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VMM)

(-) 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:471
 aligned with BACD_BACSU | P39641 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:471
                                    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       451       461       471 
           BACD_BACSU     2 ERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKYSVAVIKDKDYFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGADAITTNNELFIAPMAKACERLGLRGAGVQAAENARDKNKMRDAFNKAGVKSIKNKRVTTLEDFRAALEEIGTPLILKPTYLASSIGVTLITDTETAEDEFNRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTEGYSDYISIEGIMADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEGLGLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLLDVLCFGKDADLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEAIDIPDGLLKGDTEIVSFSAAAPGTSVDLTLFEAFNSIAAFELKGSNSQDVAESIRQIQQHAKLTAKYVLPV 472
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhheeeeee.hhhh.hhhhhh..............hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhh......eeee.hhhhhhhhhhhh...eeeee.........eee....hhhhhhhhhhhhhh.............eeeee....hhhhhh.......eeeeeeeee..eeeeeeeeee.........eeee....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeehhheeeeeeee......hhhhhhhhhhh.hhhhhhhhhhhhhhhh............eeeeeeehhhhhhhh.......eeeeeeeee..........eeeeeee....eee....hhhhh..eeeeeee.hhhhhhhhhhhhhhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vmm A   2 ERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKYSVAVIKDKDYFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGADAITTNNELFIAPMAKACERLGLRGAGVQAAENARDKNKMRDAFNKAGVKSIKNKRVTTLEDFRAALEEIGTPLILKPTYLASSIGVTLITDTETAEDEFNRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTEGYSDYISIEGIMADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEGLGLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLLDVLCFGKDADLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEAIDIPDGLLKGDTEIVSFSAAAPGTSVDLTLFEAFNSIAAFELKGSNSQDVAESIRQIQQHAKLTAKYVLPV 472
                                    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       451       461       471
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BACD_BACSU | P39641)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BACD_BACSU | P39641: 3wnz 3wo0 3wo1

(-) Related Entries Specified in the PDB File

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