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(-) Description

Title :  CRYSTAL STRUCTURE OF PARE
 
Authors :  H. Y. Jung, Y. -S. Heo
Date :  05 Feb 10  (Deposition) - 16 Feb 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A
Keywords :  Topoisomeraseiv, Pare, Novobiocin, Atp-Binding, Isomerase, Nucleotide-Binding, Topoisomerase, Isomerase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Y. Jung, Y. -S. Heo
Crystal Structure Of Pare
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TOPOISOMERASE IV SUBUNIT B
    Chains: A
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT, UNP RESIDUES 46-433
    Gene: PARE, XOO2969
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid: 291331
    Strain: KACC10331

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:16 , ASN A:86 , SER A:87 , GLU A:90 , ASP A:113 , ARG A:116 , GLY A:117 , MET A:118 , PRO A:119 , ASP A:121 , ARG A:176 , HOH A:444 , HOH A:486BINDING SITE FOR RESIDUE NOV A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:277 -Pro A:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LPS)

(-) Sequences/Alignments

Asymmetric/Biological 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:347
 aligned with Q5GYJ8_XANOR | Q5GYJ8 from UniProtKB/TrEMBL  Length:673

    Alignment length:364
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418    
         Q5GYJ8_XANOR    59 GLDPVKRRPGMYTDTARPNHLAQEVIDNSVDEALAGHAKQIEVTLYKDGSCEVSDDGRGMPVDIHPEEKIPGVELILTRLHAGGKFNNRNYTFSGGLHGVGVSVVNALSTKVELFIKREGSEHRMEFRDGNAASKLEVVGTVGKKNTGTRLRFWADPKYFDTPKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQDSWYFENGLRDYLKGEMAEHEMLPADLFVGSLKKDTEIVDWAAGWVPEGELVQESYVNLIPTAQHGTHVNGLRSGLTDALREFCDFRNLLPRGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASAR 422
               SCOP domains d3lpsa1 A:59-260 automated matches                                                                                                                                                                        d3lpsa2 A:261-422 automated matches                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------HATPase_c-3lpsA01 A:71-216                                                                                                                        ---------------------------------------------DNA_gyraseB-3lpsA02 A:262-422                                                                                                                                     Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh-----------------....hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee.....eeee....hhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeee.......eeeee..ee....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.eeeeeeee.....ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lps A  59 GLDPVKRRPGMYTDTARPNHLAQEVIDNSVDEALAGHAKQIEVTLYKDGSCEVSDDGRGMPVDIHPEEKIPGVELILTR-----------------LHGVGVSVVNALSTKVELFIKREGSEHRMEFRDGNAASKLEVVGTVGKKNTGTRLRFWADPKYFDTPKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQDSWYFENGLRDYLKGEMAEHEMLPADLFVGSLKKDTEIVDWAAGWVPEGELVQESYVNLIPTAQHGTHVNGLRSGLTDALREFCDFRNLLPRGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAAGFIEGAAHDAFSLYLNQNVEIGEKIAQIAIDRASAR 422
                                    68        78        88        98       108       118       128        |-         -      |158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418    
                                                                                                        137               155
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: His_Kinase_A (147)
(-)
Clan: no clan defined [family: DNA_gyraseB] (6)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5GYJ8_XANOR | Q5GYJ8)
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: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:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5GYJ8_XANOR | Q5GYJ8: 3lnu

(-) Related Entries Specified in the PDB File

3lnu