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(-) Description

Title :  CRYSTAL STRUCTURE OF THE XANTHOMONAS CAMPESTRIS GYRASE A C-TERMINAL DOMAIN
 
Authors :  T. J. Hsieh, T. J. Yen, T. S. Lin, H. T. Chang, S. Y. Huang, L. Farh, N. L. Chan
Date :  26 Dec 09  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gyrase A C-Terminal Domain, Gyra C-Terminal Domain, Dna Wrapping, Beta-Strand-Bearing Proline, Atp-Binding, Isomerase, Nucleotide-Binding, Topoisomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Hsieh, T. J. Yen, T. S. Lin, H. T. Chang, S. Y. Huang, L. Farh, N. L. Chan
Twisting Of The Dna Binding Surface By A Beta-Strand-Bearing Proline Modulates Dna Gyrase Activity
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT A
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN
    Gene: GYRA, XCC1574
    Mutation: YES
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Synonym: GYRA

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3L6V)

(-) Sites  (0, 0)

(no "Site" information available for 3L6V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L6V)

(-) Exons   (0, 0)

(no "Exon" information available for 3L6V)

(-) 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:313
 aligned with Q8PAB1_XANCP | Q8PAB1 from UniProtKB/TrEMBL  Length:899

    Alignment length:348
                                   539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869        
         Q8PAB1_XANCP   530 LDLIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTLLTFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPVREYADNRYVFFATRNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGESTVRSMGRTATGVRGIRLAKGEEVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAVIDVADNGDVAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGSTDEVLLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERLDASL 877
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee...eeeeeehhhhhhh.......eeee......eeeeeee....eeeeee...eeeeee.hhh.........ee.hhh........eeeeeee.......eeeeee...eeeeee.hhhh......ee.........eeeeeee....eeeeee...eeeeee.hhh.........ee.........eeeeeee...-----------------------------------.eeeeee...eeeeee.hhh.........ee..........eeeeeee....eeeeee....eeeee.hhh.........ee.........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l6v A 530 MDLIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTLLTFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPVREYADNRYVFMATRNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGESTVRSMGRTATGVRGIRLAKGEEVVSLIVSERA-----------------------------------AYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGSTDEVMLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERLDASL 877
                                   539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739|        -         -         -      |779       789       799       809       819       829       839       849       859       869        
                                                                                                                                                                                                                                            740                                 776                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with Q8PAB1_XANCP | Q8PAB1 from UniProtKB/TrEMBL  Length:899

    Alignment length:346
                                   539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869      
         Q8PAB1_XANCP   530 LDLIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTLLTFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPVREYADNRYVFFATRNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGESTVRSMGRTATGVRGIRLAKGEEVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAVIDVADNGDVAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGSTDEVLLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERLDA 875
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB01 B:827-874                 - Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB02 B:827-874                 - Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB03 B:827-874                 - Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB04 B:827-874                 - Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB05 B:827-874                 - Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB06 B:827-874                 - Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB07 B:827-874                 - Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB08 B:827-874                 - Pfam domains (8)
           Pfam domains (9) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB09 B:827-874                 - Pfam domains (9)
          Pfam domains (10) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB10 B:827-874                 - Pfam domains (10)
          Pfam domains (11) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB11 B:827-874                 - Pfam domains (11)
          Pfam domains (12) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_gyraseA_C-3l6vB12 B:827-874                 - Pfam domains (12)
         Sec.struct. author ........eeeeee...eeeeeehhhhhhh.------...hhhhh..eeeeeee....eeeeee...eeeeee.hhh.........ee.hhh........eeeeeee.......eeeeee...eeeeee.hhhh......ee.........eeeeeee....eeeeee...eeeeee.hhh.........ee.........eeeeeee..-----------------------------------..eeeeee...eeeeee.hhh.........ee..........eeeeeee....eeeeee....eeeee.hhh.........ee.........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6v B 530 MDLIAPEDVVVTLSHAGYAKRQPVSAYRAQR------SAASTKEEDFIDQLWLVNTHDTLLTFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPVREYADNRYVFMATRNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGESTVRSMGRTATGVRGIRLAKGEEVVSLIVSER-----------------------------------VAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGSTDEVMLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERLDA 875
                                   539       549       559|      569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739         -         -         -     | 779       789       799       809       819       829       839       849       859       869      
                                                        560    567                                                                                                                                                                         739                                 775
   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 3L6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L6V)

(-) Pfam Domains  (1, 12)

Asymmetric Unit
(-)
Clan: no clan defined [family: DNA_gyraseA_C] (5)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8PAB1_XANCP | Q8PAB1)
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: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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
    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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
cellular component
    GO:0009330    DNA topoisomerase complex (ATP-hydrolyzing)    Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity.
    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.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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