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(-) Description

Title :  S. AUREUS GYRB ATPASE DOMAIN IN COMPLEX WITH SMALL MOLECULE INHIBITOR
 
Authors :  P. A. Boriack-Sjodin, D. B. Prince, A. E. Eakin, B. A. Sherer
Date :  03 Oct 11  (Deposition) - 11 Jan 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein-Inhibitor Complex, Atp-Binding, Structure-Based Drug Design, Antimicrobial, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. E. Eakin, O. Green, N. Hales, G. K. Walkup, S. Bist, A. Singh, G. Mullen, J. Bryant, K. Embrey, N. Gao, A. Breeze, D. Timms, B. Andrews M. Uria-Nickelsen, J. Demeritt, J. T. Loch, K. Hull, A. Blodgett, R. N. Illingworth, B. Prince, P. A. Boriack-Sjodin, S. Hauck, L. J. Macpherson, H. Ni, B. Sherer
Pyrrolamide Dna Gyrase Inhibitors: Fragment-Based Nuclear Magnetic Resonance Screening To Identify Antibacterial Agents.
Antimicrob. Agents Chemother. V. 56 1240 2012
PubMed-ID: 22183167  |  Reference-DOI: 10.1128/AAC.05485-11

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT73.3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ATPASE DOMAIN WITH LOOP DELETION, UNP RESIDUES 14-104 AND 128-233
    Gene: GYRB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 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, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
108B2Ligand/Ion4-BROMO-5-METHYL-N-[1-(3-NITROPYRIDIN-2-YL)PIPERIDIN-4-YL]-1H-PYRROLE-2-CARBOXAMIDE
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
108B1Ligand/Ion4-BROMO-5-METHYL-N-[1-(3-NITROPYRIDIN-2-YL)PIPERIDIN-4-YL]-1H-PYRROLE-2-CARBOXAMIDE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
108B1Ligand/Ion4-BROMO-5-METHYL-N-[1-(3-NITROPYRIDIN-2-YL)PIPERIDIN-4-YL]-1H-PYRROLE-2-CARBOXAMIDE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:54 , SER A:55 , GLU A:58 , ASP A:81 , ARG A:84 , GLY A:85 , ILE A:86 , PRO A:87 , HOH A:244 , HOH A:385BINDING SITE FOR RESIDUE 08B A 1
2AC2SOFTWARETHR A:185 , ASN B:54 , SER B:55 , GLU B:58 , ASP B:81 , ARG B:84 , GLY B:85 , ILE B:86 , PRO B:87 , ILE B:175 , HOH B:253 , HOH B:279 , HOH B:374BINDING SITE FOR RESIDUE 08B B 2
3AC3SOFTWAREGLY A:208 , HIS A:228 , HOH A:282 , HOH A:327 , HOH A:379 , HOH A:380BINDING SITE FOR RESIDUE MG A 234
4AC4SOFTWAREASN B:54 , HOH B:308 , HOH B:318 , HOH B:351 , HOH B:383BINDING SITE FOR RESIDUE MG B 1
5AC5SOFTWAREGLY B:208 , HIS B:228 , HOH B:294 , HOH B:313 , HOH B:333BINDING SITE FOR RESIDUE MG B 234
6AC6SOFTWAREGLU A:164 , HOH A:283 , HOH A:337 , LEU B:60 , HOH B:247 , HOH B:290BINDING SITE FOR RESIDUE MG A 235

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U2D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U2D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U2D)

(-) Exons   (0, 0)

(no "Exon" information available for 3U2D)

(-) 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:194
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:217
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
           GYRB_STAAU    14 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3u2da_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhh-----------------------hhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u2d A  14 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    23        33        43        53        63        73        83        93       103|        -         -    |  133       143       153       163       173       183       193       203       213       223       
                                                                                                                    104                     128                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with GYRB_STAAU | P0A0K8 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:211
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
           GYRB_STAAU    20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
               SCOP domains d3u2db_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeee...........--..hhhhhhhh-----------------------.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u2d B  20 QVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQE--GRPAVEVILT-----------------------SSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    29        39        49        59        69        79        89  |  |  99    |    -         -       129       139       149       159       169       179       189       199       209       219       229 
                                                                                                   92 95      104                     128
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U2D)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GYRB_STAAU | P0A0K8)
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: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.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
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_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2k 4plb 4urm 4uro 5bs3 5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

3ttz 3u2k