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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE)
 
Authors :  S. Classen, S. Olland, J. M. Berger
Date :  17 Sep 03  (Deposition) - 30 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ghkl Atpase Domain, Icrf, Icrf-187, Dexrazoxane, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Classen, S. Olland, J. M. Berger
Structure Of The Topoisomerase Ii Atpase Region And Its Mechanism Of Inhibition By The Chemotherapeutic Agent Icrf-187
Proc. Natl. Acad. Sci. Usa V. 100 10629 2003
PubMed-ID: 12963818  |  Reference-DOI: 10.1073/PNAS.1832879100

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE II
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL ATPASE REGION
    Gene: TOP2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CDX1Ligand/Ion(S)-4,4'-(1-METHYL-1,2-ETHANEDIYL)BIS-2,6-PIPERAZINEDIONE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:70 , ANP A:902 , HOH A:905 , HOH A:937BINDING SITE FOR RESIDUE MG A 904
2AC2SOFTWAREASN B:70 , ANP B:903 , HOH B:910 , HOH B:911BINDING SITE FOR RESIDUE MG B 905
3AC3SOFTWAREHIS A:20 , THR A:27 , TYR A:28 , ASN A:142 , TYR A:144 , GLN A:365 , HIS B:20 , THR B:27 , TYR B:28 , ASN B:142 , TYR B:144 , GLN B:365BINDING SITE FOR RESIDUE CDX B 901
4AC4SOFTWAREGLU A:66 , ASN A:70 , ASN A:74 , ARG A:77 , ASN A:99 , ILE A:104 , ILE A:120 , PHE A:121 , SER A:127 , SER A:128 , ASN A:129 , GLY A:140 , ARG A:141 , ASN A:142 , GLY A:143 , TYR A:144 , GLY A:145 , ALA A:146 , LYS A:147 , GLN A:365 , LYS A:367 , MG A:904 , HOH A:905 , HOH A:907 , HOH A:909 , HOH A:911 , HOH A:912 , HOH A:930 , HOH A:937 , HOH A:1030 , TYR B:12 , HOH B:929BINDING SITE FOR RESIDUE ANP A 902
5AC5SOFTWARETYR A:12 , HOH A:1047 , GLU B:66 , ASN B:70 , ASN B:74 , ASN B:99 , ILE B:104 , ILE B:120 , PHE B:121 , SER B:127 , SER B:128 , ASN B:129 , GLY B:140 , ARG B:141 , ASN B:142 , GLY B:143 , TYR B:144 , GLY B:145 , ALA B:146 , LYS B:147 , GLN B:365 , LYS B:367 , MG B:905 , HOH B:910 , HOH B:911 , HOH B:927 , HOH B:931 , HOH B:941 , HOH B:960BINDING SITE FOR RESIDUE ANP B 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QZR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QZR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QZR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QZR)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL088W1YNL088W.1XIV:457706-4619924287TOP2_YEAST1-142814282A:7-410 (gaps)
B:8-405 (gaps)		404
398

(-) 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:382
 aligned with TOP2_YEAST | P06786 from UniProtKB/Swiss-Prot  Length:1428

    Alignment length:404
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406    
           TOP2_YEAST     7 SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADANEEN 410
               SCOP domains d1qzra2 A:7-245 DNA topoisomerase II                                                                                                                                                                                                           d1qzra1 A:246                 -410 DNA topoisomerase II                                                                                                               SCOP domains
               CATH domains --------1qzrA01 A:15-258  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                ---1qzrA02 A:279-406  [code=3.30.230.10, no name defined]                                                                          ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhee.hhhhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee..............hhhhhhhhh..ee................hhhhhhhhheeeeeeeeee....eeeeeeee....ee...eeee......eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh...eeee..ee....hhhhhhhh.....-----------------....eeeeee..eeeeeee.....eeeeee..ee....hhhhhhhhhhhhhhhhhhhh.-----.hhhhhhh.eeeeeee.................hhhhh......hhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:7-410 (gaps) UniProt: 1-1428 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                 1qzr A   7 SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSL-----------------IPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKK-----VKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADANEEN 410
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 |       -       276       286       296       306       316       326       | -   |   346       356       366       376       386       396       406    
                                                                                                                                                                                                                                                                                     258               276                                                       334   340                                                                      


Chain B from PDB  Type:PROTEIN  Length:378
 aligned with TOP2_YEAST | P06786 from UniProtKB/Swiss-Prot  Length:1428

    Alignment length:398
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
           TOP2_YEAST     8 ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIAD 405
               SCOP domains d1qzrb2 B:8-245 DNA topoisomerase II                                                                                                                                                                                                          d1qzrb1 B:246-4               05 DNA topoisomerase II                                                                                                            SCOP domains
               CATH domains -------1qzrB01 B:15-258  [code=3.30.565.10, no name defined]                                                                                                                                                                                               --               ---1qzrB02 B:279-405  [code=3.30.230.10, no name defined]                                                                          CATH domains
           Pfam domains (1) -----------------------------------------------HATPase_c-1qzrB01 B:55-204                                                                                                                            -----------------------------------------DNA_gyraseB-1qz               rB03 B:246-405                                                                                                                     Pfam domains (1)
           Pfam domains (2) -----------------------------------------------HATPase_c-1qzrB02 B:55-204                                                                                                                            -----------------------------------------DNA_gyraseB-1qz               rB04 B:246-405                                                                                                                     Pfam domains (2)
         Sec.struct. author .....ee.hhhhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee..............hhhhhhhhh..ee................hhhhhhhhheeeeeeeeee....eeeeeeee....ee...eeee......eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhh...eeee..ee....hhhhhhhhhhhhhhh---------------....eeeeee..eeeeeee.....eeeeee..ee....hhhhhhhhhhhhhhhhhhhhh-----.hhhhhhh.eeeeeee.................hhhhh......hhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:8-405 (gaps) UniProt: 1-1428 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1qzr B   8 ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEK---------------IPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKKISEILKK-----VKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIAD 405
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257  |      -       277       287       297       307       317       327      |  -  |    347       357       367       377       387       397        
                                                                                                                                                                                                                                                                                      260             276                                                       334   340
   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, 4)

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

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TOP2_YEAST | P06786)
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: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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006271    DNA strand elongation involved in DNA replication    The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
    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:0006333    chromatin assembly or disassembly    The formation or destruction of chromatin structures.
    GO:0031055    chromatin remodeling at centromere    Dynamic structural changes in centromeric DNA.
    GO:0044774    mitotic DNA integrity checkpoint    A mitotic cell cycle process that controls cell cycle progression in response to changes in DNA structure by monitoring the integrity of the DNA. The DNA integrity checkpoint begins with detection of DNA damage, defects in DNA structure or DNA replication, and ends with signal transduction.
    GO:0007131    reciprocal meiotic recombination    The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
    GO:0000019    regulation of mitotic recombination    Any process that modulates the frequency, rate or extent of DNA recombination during mitosis.
    GO:0097046    replication fork progression beyond termination site    Regulation of DNA replication by a mechanism that allows a DNA replication fork to progress beyond a termination site, which is a region containing fork pausing elements that influence the progression and merging of DNA replication forks.
    GO:0000712    resolution of meiotic recombination intermediates    The cleavage and rejoining of intermediates, such as Holliday junctions, formed during meiotic recombination to produce two intact molecules in which genetic material has been exchanged.
    GO:0000819    sister chromatid segregation    The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets.
cellular component
    GO:0097047    DNA replication termination region    A chromosomal region that contains fork pausing elements influencing the progression and merging of DNA replication forks.
    GO:0009330    DNA topoisomerase complex (ATP-hydrolyzing)    Complex that possesses DNA topoisomerase (ATP-hydrolyzing) activity.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0000795    synaptonemal complex    A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.

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  1qzr
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  TOP2_YEAST | P06786
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP2_YEAST | P06786: 1bgw 1bjt 1pvg 2rgr 3l4j 3l4k 4gfh

(-) Related Entries Specified in the PDB File

1bgw SACCHAROMYCES CEREVISIAE TOPOISOMERASE II RESIDUES 410-1202
1bjt SACCHAROMYCES CEREVISIAE TOPOISOMERASE II RESIDUES 409-1201
1pvg CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II WITHOUT ICRF-187