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(-)Asym./Biol. Unit
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(-) Description

Title :  REVERSE GYRASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  A. C. Rodriguez, D. Stock
Date :  21 Aug 01  (Deposition) - 11 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  B
Keywords :  Topoisomerase, Dna Supercoiling, Archaea, Helicase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Rodriguez, D. Stock
Crystal Structure Of Reverse Gyrase: Insights Into The Positive Supercoiling Of Dna.
Embo J. V. 21 418 2002
PubMed-ID: 11823434  |  Reference-DOI: 10.1093/EMBOJ/21.3.418

(-) Compounds

Molecule 1 - REVERSE GYRASE
    Atcc: 49558
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRET3A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSMZ)
    Strain: VC-16
    Synonym: TOP-RG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1GKU)

(-) Sites  (0, 0)

(no "Site" information available for 1GKU)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:35 -B:650

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.RGYR_ARCFU506-662  1B:506-662

(-) Exons   (0, 0)

(no "Exon" information available for 1GKU)

(-) 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 B from PDB  Type:PROTEIN  Length:1011
 aligned with RGYR_ARCFU | O29238 from UniProtKB/Swiss-Prot  Length:1054

    Alignment length:1054
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050    
          RGYR_ARCFU      1 MIPVVYSNLCPVCGGDLESKEIEKHVCFRKKRSLCLFPEDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDIGSSRITVRNVEDVAVNDESISTLSSILEKLGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKLYDIEFKSIDEVDFEKLSRELDESRDRYRRRQEFDLIKPALFIVESPTKARQISRFFGKPSVKVLDGAVVYEIPMQKYVLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTPVLGWIIDRFQESRERRKIAIVRDFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGESGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKNELPTGTFRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIERGELDYLKALEDLYAEIKSID 1054
               SCOP domains d1gkub 1 B:1 -250 Hel           icase-like domain of reverse gyrase                                                                                                                                                                                       d1gkub2 B:251-498 Helicase-like domain of reverse gyrase                                                                                                                                                                                                d1gkub3 B:499-1054 Topoisomerase domain of reverse gyrase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------ ----- --------           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1gkuB03 B:246-352,B:426-504 P-loop containing nucleotide triphosphate hydrolases                           -------------------------------------------------------------------------1gkuB03 B:246-352,B:426-504                                                    1gkuB05 B:505-555,B:608-677                        ---------------------------                        -1gkuB05 B:505-555,B:608-677  [code=3.40.50.140, no name defined]      1gkuB06 B:678-732,B:954-1054 Topoisomerase I, domain 2 ---------------------------------------1gkuB08 B:772-890 Topoisomerase I, domain 4                                                                            ---------------------------------------------------------------1gkuB06 B:678-732,B:954-1054 Topoisomerase I, domain 2                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-..ee.-....ee..-----------......hhhhhhhhhhhhhh.....hhhhhhhhhhhhh...ee........hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh....hhhh.eee......hhhhhhhhhhhhhh.eeeeehhhhhhh........eeee.hhhhhhh.hhhhhhhhhhh.eeee....eeee....eeee.........hhhhhhhhhh......ee....eeeeee.......hhhhhh.....eeeee.hhhhhhhhhhh......eee.....hhhhhhhhh....eeeee..------..........eeeee...eeeee..hhhhhhhhhhhhhhh...hhhhhhh.......hhhhhhhhhhhhhh.........eee..eeeeehhhhhhhhhhh...ee..ee..eeeeee..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhh..ee.eeeee..eeeeeee...eeeeeee.....eee.................eeee..------------------------.hhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhh...eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.eeeeeee....eee.....eeeeeeeeeeeeeeee......hhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhhhh.......................hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeee..eeeeehhhhhhh...........eeeeee...eeee.....hhhhhhhhhhhhh.....hhhhhhhhhhhh..eeee..eeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPRIM  PDB: B:506-662 UniProt: 506-662                                                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gku B    1 AAAAAA-AAAAA-AAAAAAAA-----------SLCLFPEDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDIGSSRITVRNVEDVAVNDESISTLSSILEKLGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGDYEKFVEGEIDHLIGTAH------RGLDLPERIRFAVFVGCPSFRVTIEDIDSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQAKDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSAFIERAKLYDIEFKSIDEVDFEKLSRELDESRDRYRRRQEFDLIKPALFIVESPTKARQISRFFGKPSVKVLDGAVVYEIPMQKYVLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYASIK------------------------DNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLVLGWIIDRFQESRERRKIAIVRDFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGESGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKNELPTGTFRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIERGELDYLKALEDMYAEIKSID 1054
                                 | |10 | |    20|        -  |     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       | -    |  340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580 |       -         -      |610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050    
                                 6 8  12 |     21          33                                                                                                                                                                                                                                                                                                    328    335                                                                                                                                                                                                                                                    582                      607                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                        14
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GKU)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (RGYR_ARCFU | O29238)
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:0003917    DNA topoisomerase type I activity    Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
    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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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: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.

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  RGYR_ARCFU | O29238
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 Related Entries

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

UniProtKB/Swiss-Prot
        RGYR_ARCFU | O29238: 1gl9

(-) Related Entries Specified in the PDB File

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