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(-) Description

Title :  CRYSTAL STRUCTURE OF BIOTIN-PROTEIN LIGASE BIRA FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH AN ACYLSULFAMIDE BISUBSTRATE INHIBITOR
 
Authors :  T. W. Geders, B. C. Finzel
Date :  05 May 11  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Biotin-Protein Ligase, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. P. Duckworth, T. W. Geders, D. Tiwari, H. I. Boshoff, P. A. Sibbald, C. E. Barry, D. Schnappinger, B. C. Finzel, C. C. Aldrich
Bisubstrate Adenylation Inhibitors Of Biotin Protein Ligase From Mycobacterium Tuberculosis.
Chem. Biol. V. 18 1432 2011
PubMed-ID: 22118677  |  Reference-DOI: 10.1016/J.CHEMBIOL.2011.08.013

(-) Compounds

Molecule 1 - BIRA BIFUNCTIONAL PROTEIN
    Chains: A, B
    EC Number: 6.3.4.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28B
    Expression System Strain: MACH I
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BIRA, MT3379, RV3279C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BS52Ligand/Ion5'-DEOXY-5'-[({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}SULFAMOYL)AMINO]ADENOSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BS51Ligand/Ion5'-DEOXY-5'-[({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}SULFAMOYL)AMINO]ADENOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BS51Ligand/Ion5'-DEOXY-5'-[({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}SULFAMOYL)AMINO]ADENOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:38 , THR A:39 , ASN A:40 , GLN A:63 , GLY A:66 , ARG A:67 , GLY A:68 , ARG A:69 , ARG A:72 , GLY A:73 , TRP A:74 , ALA A:75 , GLN A:81 , ILE A:83 , ASN A:130 , LYS A:138 , GLY A:141 , ILE A:142 , LEU A:143 , VAL A:155 , GLY A:156 , ASN A:158 , VAL A:166 , ASP A:167 , ALA A:170 , HOH A:289 , HOH A:382 , HOH A:531BINDING SITE FOR RESIDUE BS5 A 1001
2AC2SOFTWAREHOH A:334 , SER B:38 , THR B:39 , ASN B:40 , GLN B:63 , GLY B:66 , ARG B:67 , GLY B:68 , ARG B:69 , ARG B:72 , GLY B:73 , TRP B:74 , ALA B:75 , GLN B:81 , ILE B:83 , ASN B:130 , LYS B:138 , GLY B:141 , ILE B:142 , VAL B:155 , GLY B:156 , ASN B:158 , VAL B:166 , ASP B:167 , ALA B:170 , HOH B:322 , HOH B:339 , HOH B:384 , HOH B:501BINDING SITE FOR RESIDUE BS5 B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:128 -Pro A:129
2Gln A:148 -Pro A:149
3Trp B:128 -Pro B:129
4Gln B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RUX)

(-) 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:265
 aligned with P96884_MYCTO | P96884 from UniProtKB/TrEMBL  Length:266

    Alignment length:265
                                    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     
         P96884_MYCTO     2 TDRDRLRPPLDERSLRDQLIGAGSGWRQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVGVRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAVPPAETGLKWPNDVLARGGKLAGILAEVAQPFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQWRNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRTVVVSAGDVVHLR 266
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...hhhhhhhhhh.......eeeeeeee.hhhhhhhhhhhh......eeeeeeee..ee.hhh.ee......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.......eee...eeee..eeeeeeeeeee..eeeeeeeee...hhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeeee.....eeeeeeeee.....eeeee..eeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rux A   2 TDRDRLRPPLDERSLRDQLIGAGSGWRQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVGVRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAVPPAETGLKWPNDVLARGGKLAGILAEVAQPFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQWRNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRTVVVSAGDVVHLR 266
                                    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     


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with P96884_MYCTO | P96884 from UniProtKB/TrEMBL  Length:266

    Alignment length:263
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   
         P96884_MYCTO     4 RDRLRPPLDERSLRDQLIGAGSGWRQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVGVRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAVPPAETGLKWPNDVLARGGKLAGILAEVAQPFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQWRNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRTVVVSAGDVVHLR 266
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhh.......eeeeeeee.hhhhhhhhhhhh......eeeeeeee..ee.hhh.ee......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.....--...eee...eeee..eeeeeeeeeee..eeeeeeeee...hhhhhh..............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....eeeeehhhhh.eeeeeeee.....eeeee..eeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rux B   4 RDRLRPPLDERSLRDQLIGAGSGWRQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVGVRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAV--AETGLKWPNDVLARGGKLAGILAEVAQPFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQWRNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRTVVVSAGDVVHLR 266
                                    13        23        33        43        53        63        73        83        93       103       113     | 123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   
                                                                                                                                             119  |                                                                                                                                                
                                                                                                                                                122
   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 3RUX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P96884_MYCTO | P96884)
molecular function
    GO:0004077    biotin-[acetyl-CoA-carboxylase] ligase activity    Catalysis of the reaction: ATP + biotin + apo-(acetyl-CoA:carbon-dioxide ligase (ADP forming)) = AMP + diphosphate + (acetyl-CoA:carbon-dioxide ligase (ADP forming)).
    GO:0018271    biotin-protein ligase activity    Catalysis of the reaction: ATP + biotin + protein = AMP + diphosphate + biotin-protein.
    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.
biological process
    GO:0006768    biotin metabolic process    The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0009305    protein biotinylation    The addition of biotin (vitamin B7 / vitamin H) to a protein amino acid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        P96884_MYCTO | P96884: 4op0
UniProtKB/TrEMBL
        P96884_MYCTO | P96884: 2cgh 3l1a 3l2z

(-) Related Entries Specified in the PDB File

2cgh 3l1a 3l2z