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(-) Description

Title :  STRUCTURE OF THE M. SMEGMATIS GYRB ATPASE DOMAIN IN COMPLEX WITH AN AMINOPYRAZINAMIDE
 
Authors :  J. A. Tucker, P. S. Shirude, P. Madhavapeddi, S. Hussein, R. Basu, S. Gho
Date :  09 Aug 12  (Deposition) - 23 Jan 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Isomerase, Dna Topoisomerase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Shirude, P. Madhavapeddi, J. A. Tucker, K. Murugan, V. Patil, H. Basavarajappa, A. V. Raichurkar, V. Humnabadkar, S. Hussein, S. Sharma, V. K. Ramya, C. B. Narayan, T. S. Balganesh, V. K. Sambandamurthy
Aminopyrazinamides: Novel And Specific Gyrb Inhibitors That Kill Replicating And Nonreplicating Mycobacterium Tuberculosis.
Acs Chem. Biol. V. 8 519 2013
PubMed-ID: 23268609  |  Reference-DOI: 10.1021/CB300510W

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Fragment: ATPASE DOMAIN, RESIDUES 9-102,123-213,246-255
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1B5U2Ligand/Ion6-(3,4-DIMETHYLPHENYL)-3-[[4-[3-(4-METHYLPIPERAZIN-1-YLPHENYL]AMINO]PYRAZINE-2-CARBOXAMIDE
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1B5U1Ligand/Ion6-(3,4-DIMETHYLPHENYL)-3-[[4-[3-(4-METHYLPIPERAZIN-1-YLPHENYL]AMINO]PYRAZINE-2-CARBOXAMIDE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1B5U1Ligand/Ion6-(3,4-DIMETHYLPHENYL)-3-[[4-[3-(4-METHYLPIPERAZIN-1-YLPHENYL]AMINO]PYRAZINE-2-CARBOXAMIDE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:52 , GLU A:56 , ASP A:79 , ARG A:82 , GLY A:83 , ILE A:84 , PRO A:85 , ASP A:97 , GLN A:102 , SER A:126 , THR A:169 , HOH A:2007 , HOH A:2020 , HOH A:2030 , GLN B:195 , PHE B:199 , TYR B:253BINDING SITE FOR RESIDUE B5U A1256
2AC2SOFTWAREGLN A:195 , TYR A:253 , GLU B:48 , ASN B:52 , GLU B:56 , ASP B:79 , ARG B:82 , GLY B:83 , ILE B:84 , PRO B:85 , THR B:95 , VAL B:99 , MET B:100 , SER B:126 , HOH B:2004 , HOH B:2019 , HOH B:2034BINDING SITE FOR RESIDUE B5U B1256
3AC3SOFTWAREASP A:80 , GLY A:81 , THR A:167 , HOH A:2041 , HOH A:2042BINDING SITE FOR RESIDUE NA A1257
4AC4SOFTWAREASP B:80 , GLY B:81 , THR B:167 , HOH B:2010 , HOH B:2011 , HOH B:2043 , HOH B:2044BINDING SITE FOR RESIDUE NA B1257

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B6C)

(-) Exons   (0, 0)

(no "Exon" information available for 4B6C)

(-) 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:161
 aligned with GYRB_MYCS2 | A0QNE0 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:220
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
           GYRB_MYCS2    36 STGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMHATGMPTIDVVMTQLHAGGKFDGETYAVSGGLHGVGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERVTAEEVVDDVVKDTAEAPKTADEKAAEATGPSKVKHRVFHYPG 255
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee.......-------.....hhhh--------------------hhhhhhhhheeeeeeeeee..eeeeeeee..ee...eeeee....eeeeeeee..........hhhhhhhhhhhhhhhh...eeeeee...--------------------------------..eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6c A  36 STGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPV-------PTIDVVMTQ--------------------VGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERD--------------------------------GKHRVFHYPG 255
                                    45        55        65        75        85|       95      |  -         -       125       135       145       155       165       175       185       195       205       | -         -         -         -|      255
                                                                             86      94     102                  123                                                                                       213                              246         


Chain A from PDB  Type:PROTEIN  Length:161
 aligned with GYRB_MYCSM | P0C559 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:220
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
           GYRB_MYCSM    36 STGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMHATGMPTIDVVMTQLHAGGKFDGETYAVSGGLHGVGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERVTAEEVVDDVVKDTAEAPKTADEKAAEATGPSKVKHRVFHYPG 255
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee.......-------.....hhhh--------------------hhhhhhhhheeeeeeeeee..eeeeeeee..ee...eeeee....eeeeeeee..........hhhhhhhhhhhhhhhh...eeeeee...--------------------------------..eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6c A  36 STGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPV-------PTIDVVMTQ--------------------VGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERD--------------------------------GKHRVFHYPG 255
                                    45        55        65        75        85|       95      |  -         -       125       135       145       155       165       175       185       195       205       | -         -         -         -|      255
                                                                             86      94     102                  123                                                                                       213                              246         


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with GYRB_MYCS2 | A0QNE0 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:219
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         
           GYRB_MYCS2    37 TGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMHATGMPTIDVVMTQLHAGGKFDGETYAVSGGLHGVGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERVTAEEVVDDVVKDTAEAPKTADEKAAEATGPSKVKHRVFHYPG 255
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee..............hhhhhhhh.--------------------.........eeeeeeeeee..eeeeeeee..ee...eeeee....eeeeeeeehhhhhh....hhhhhhhhhhhhhhhh...eeeeee...--------------------------------..eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6c B  37 TGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMHATGMPTIDVVMTQ--------------------VGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERD--------------------------------GKHRVFHYPG 255
                                    46        56        66        76        86        96     |   -         -      |126       136       146       156       166       176       186       196       206      |  -         -         -       246         
                                                                                           102                  123                                                                                       213                              246         


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with GYRB_MYCSM | P0C559 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:219
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246         
           GYRB_MYCSM    37 TGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMHATGMPTIDVVMTQLHAGGKFDGETYAVSGGLHGVGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERVTAEEVVDDVVKDTAEAPKTADEKAAEATGPSKVKHRVFHYPG 255
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee..............hhhhhhhh.--------------------.........eeeeeeeeee..eeeeeeee..ee...eeeee....eeeeeeeehhhhhh....hhhhhhhhhhhhhhhh...eeeeee...--------------------------------..eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b6c B  37 TGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMHATGMPTIDVVMTQ--------------------VGVSVVNALSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYNFETVARRLQEMAFLNKGLTIELTDERD--------------------------------GKHRVFHYPG 255
                                    46        56        66        76        86        96     |   -         -      |126       136       146       156       166       176       186       196       206      |  -         -         -       246         
                                                                                           102                  123                                                                                       213                              246
   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 4B6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B6C)

(-) Gene Ontology  (13, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GYRB_MYCS2 | A0QNE0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034335    DNA supercoiling activity    Catalytic introduction of supercoils in a DNA molecule or region thereof. In bacteria, negative supercoils are only introduced by DNA gyrase, a type II topoisomerase, but not all DNA gyrases are capable of introducing supercoils. In bacteria, the level of supercoiling varies widely between species and has been characterized properly in only a handful of organisms. The best characterized enzyme, from E.coli, is exceptionally proficient at supercoiling and this ability is not representative of all bacteria.
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B   (GYRB_MYCSM | P0C559)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034335    DNA supercoiling activity    Catalytic introduction of supercoils in a DNA molecule or region thereof. In bacteria, negative supercoils are only introduced by DNA gyrase, a type II topoisomerase, but not all DNA gyrases are capable of introducing supercoils. In bacteria, the level of supercoiling varies widely between species and has been characterized properly in only a handful of organisms. The best characterized enzyme, from E.coli, is exceptionally proficient at supercoiling and this ability is not representative of all bacteria.
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003918    DNA topoisomerase type II (ATP-hydrolyzing) activity    Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRB_MYCS2 | A0QNE0: 4bae
        GYRB_MYCSM | P0C559: 4bae

(-) Related Entries Specified in the PDB File

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