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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS BIOTIN LIGASE COMPLEXED WITH BISUBSTRATE INHIBITOR 82 THAT INCORPORATES A MORPHOLINE IN PLACE OF THE RIBOSE
 
Authors :  T. De La Mora-Rey, B. C. Finzel
Date :  24 Jan 15  (Deposition) - 02 Sep 15  (Release) - 07 Oct 15  (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, Bisubstrate Inhibitor, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Bockman, A. S. Kalinda, R. Petrelli, T. De La Mora-Rey, D. Tiwari, F. Liu, S. Dawadi, M. Nandakumar, K. Y. Rhee, D. Schnappinger, B. C. Finzel, C. C. Aldrich
Targeting Mycobacterium Tuberculosis Biotin Protein Ligase (Mtbpl) With Nucleoside-Based Bisubstrate Adenylation Inhibitors.
J. Med. Chem. V. 58 7349 2015
PubMed-ID: 26299766  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00719

(-) Compounds

Molecule 1 - BIFUNCTIONAL LIGASE/REPRESSOR BIRA
    Chains: A, B
    EC Number: 6.3.4.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: MACH I
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BIRA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_01710, IQ44_01750, IQ45_01765, IQ46_01705, IQ47_01735, IQ48_01770, IU12_01860, IU13_01785, IU14_01730, IU16_01770, IU17_01745, IU18_01730, IU19_01775, IU20_01750, IU22_01755, IU23_01750, IU24_01735, IZ84_17515, JE53_17495, LJ70_17695, T209_01770
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: BIOTIN--ACETYL-COA-CARBOXYLASE LIGASE,BIOTIN-PROTEIN LIGASE, BIRA PROTEIN

 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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
144O2Ligand/Ion[(2S,6R)-6-(6-AMINO-9H-PURIN-9-YL)MORPHOLIN-2-YL]METHYL{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}SULFAMATE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
144O1Ligand/Ion[(2S,6R)-6-(6-AMINO-9H-PURIN-9-YL)MORPHOLIN-2-YL]METHYL{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}SULFAMATE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
144O1Ligand/Ion[(2S,6R)-6-(6-AMINO-9H-PURIN-9-YL)MORPHOLIN-2-YL]METHYL{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}SULFAMATE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
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 , LYS A:138 , GLY A:141 , ILE A:142 , VAL A:155 , GLY A:156 , ASN A:158 , VAL A:166 , ASP A:167 , ALA A:170 , HOH A:519 , HOH A:565binding site for residue 44O A 301
2AC2SOFTWAREPRO A:120 , PRO A:121 , ALA A:122 , GLU A:123 , THR A:124binding site for residue EDO A 302
3AC3SOFTWAREHIS A:70 , ARG A:72 , GLU A:226 , PRO A:228 , ASP A:261binding site for residue DMS A 303
4AC4SOFTWARESER 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 , 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:540 , HOH B:715binding site for residue 44O B 301
5AC5SOFTWAREGLU A:193 , GLY B:220 , ARG B:222binding site for residue DMS B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XU1)

(-) 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 4XU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XU1)

(-) Exons   (0, 0)

(no "Exon" information available for 4XU1)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...hhhhhhhhhh.......eeeeeeee.hhhhhhhhhhhh......eeeeeeee..ee.hhh.ee......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.......eee...eeee..eeeeeeeeeee..eeeeeeeee...hhhhhh.....hhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....eeeee.....eeeeeeeee.....eeeee..eeeee...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xu1 A   3 DRDRLRPPLDERSLRDQLIGAGSGWRQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVGVRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAVPPAETGLKWPNDVLARGGKLAGILAEVAQPFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQWRNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRTVVVSAGDVVHL 265
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262   


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhh.......eeeee....hhhhhhhhhhhh......eeeee.....ee.hhh.ee......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee...eeee..eeeeeeeeeee..eeeeeeeee...hhhhh...............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....eeeeee...eeeeeeeeee.....eeeee..eeeee....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xu1 B   4 RDRLRPPLDERSLRDQLIGAGSGWRQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVGVRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAVPPAETGLKWPNDVLARGGKLAGILAEVAQPFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQWRNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCLDVGGRTVVVSAGDVVHLR 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
   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 4XU1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XU1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XU1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        I6YFP0_MYCTU | I6YFP0: 4op0 4xtu 4xtv 4xtw 4xtx 4xty 4xtz 4xu0 4xu2 4xu3

(-) Related Entries Specified in the PDB File

4xtu 4xtv 4xtw 4xtx 4xty 4xtz 4xu0 4xu2 4xu3