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(-) Description

Title :  APO STRUCTURE OF THE HEL308 SUPERFAMILY 2 HELICASE
 
Authors :  K. Buettner, S. Nehring, K. P. Hopfner
Date :  19 Mar 07  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.14
Chains :  Asym./Biol. Unit :  A
Keywords :  Archaeal Helicase, Sf2 Helicase, Dna Repair, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Buttner, S. Nehring, K. P. Hopfner
Structural Basis For Dna Duplex Separation By A Superfamily-2 Helicase.
Nat. Struct. Mol. Biol. V. 14 647 2007
PubMed-ID: 17558417  |  Reference-DOI: 10.1038/NSMB1246
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AFUHEL308 HELICASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-29
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1PO410Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:54 , LEU A:55 , GLU A:58 , SER A:87 , LYS A:90BINDING SITE FOR RESIDUE PO4 A 703
02AC2SOFTWAREILE A:640 , GLY A:641 , ARG A:642 , VAL A:643 , ARG A:644BINDING SITE FOR RESIDUE PO4 A 704
03AC3SOFTWAREARG A:638 , ARG A:644 , PO4 A:709BINDING SITE FOR RESIDUE PO4 A 705
04AC4SOFTWAREASP A:151 , ARG A:404 , THR A:406 , LYS A:408BINDING SITE FOR RESIDUE PO4 A 706
05AC5SOFTWAREARG A:78 , LYS A:154 , ARG A:155BINDING SITE FOR RESIDUE PO4 A 707
06AC6SOFTWAREALA A:50 , LEU A:80 , LYS A:84 , ASP A:145 , GLU A:146BINDING SITE FOR RESIDUE PO4 A 708
07AC7SOFTWAREILE A:637 , ARG A:638 , HIS A:639 , ILE A:640 , ARG A:644 , PO4 A:705BINDING SITE FOR RESIDUE PO4 A 709
08AC8SOFTWAREGLU A:621 , LYS A:624 , HIS A:625 , ARG A:636BINDING SITE FOR RESIDUE PO4 A 710
09AC9SOFTWAREARG A:516 , TYR A:545 , SER A:548 , PHE A:550 , TRP A:556 , GLU A:560BINDING SITE FOR RESIDUE PO4 A 711
10BC1SOFTWAREARG A:252 , HIS A:303 , ALA A:304 , THR A:329 , THR A:331BINDING SITE FOR RESIDUE PO4 A 712

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P6U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P6U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P6U)

(-) Exons   (0, 0)

(no "Exon" information available for 2P6U)

(-) 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:671
 aligned with HELS_ARCFU | P0DMI1 from UniProtKB/Swiss-Prot  Length:691

    Alignment length:686
                                    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      
           HELS_ARCFU     1 MKVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIFGEPERITSKLGVETHLRFHSLSIICDGYAKTLEELEDFFADTFFFKQNEISLSYELERVVRQLENWGMVVEDHHLAPTKLGSLVSRLYIDPLTGFIFHDVLSRMELSDIGALHLICRTPDMERLTVRKTDSWVEEEAFRLRKELSYYPSDFSVEYDWFLSEVKTALCLKDWIEEKDEDEICAKYGIAPGDLRRIVETAEWLSNAMNRIAEEVGNTSVSGLTERIKHGVKEELLELVRIRHIGRVRARKLYNAGIRNAEDIVRHREKVASLIGRGIAERVVEGISVKS 686
               SCOP domains d2p6ua3 A:1-202 a        utomated matches                                                                                                                                                                 d2p6ua4 A:203-403 automated matches                                                                                                                                                                      d2p6ua1 A:404-488 automated matches                                                  d2p6ua2 A:489-686 automated matches                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..--------.....hhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh....eee..........hhhhh.eeeeehhhhhhhhhh...hhhhh.eeee.hhhhhhh..hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhh.eeee........eeeeee..eeeeee..eee....hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhh...eeee....---......eeee......----...hhhhhhhhhh...........eeeee.....hhhhhhh..............hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eee...eeehhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh..............hhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh....hhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p6u A   1 MKVEELAESISSYAVGI--------LFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTL---VNLPARRVIVRSLYRF----KRIKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIFGEPERITSKLGVETHLRFHSLSIICDGYAKTLEELEDFFADTFFFKQNEISLSYELERVVRQLENWGMVVEAAHLAPTKLGSLVSRLYIDPLTGFIFHDVLSRMELSDIGALHLICRTPDMERLTVRKTDSWVEEEAFRLRKELSYYPSDFSVEYDWFLSEVKTALCLKDWIEEKDEDEICAKYGIAPGDLRRIVETAEWLSNAMNRIAEEVGNTSVSGLTERIKHGVKEELLELVRIRHIGRVRARKLYNAGIRNAEDIVRHREKVASLIGRGIAERVVEGISVKS 686
                                    10      |  -     |  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      
                                           17       26                                                                                                                                                                                                                                                                                                               332 336            351  356
   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  (3, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P6U)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HELS_ARCFU | P0DMI1)
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: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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    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.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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 Related Entries

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        HELS_ARCFU | P0DMI1: 2p6r

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