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(-) Description

Title :  STRUCTURE OF DNA HELICASE MUTANT WITH ADPNP
 
Authors :  P. Soultanas, M. S. Dillingham, S. S. Velankar, D. B. Wigley
Date :  14 May 99  (Deposition) - 13 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Repair, Dna Replication, Sos Response, Helicase, Atp- Binding, Dna-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Soultanas, M. S. Dillingham, S. S. Velankar, D. B. Wigley
Dna Binding Mediates Conformational Changes And Metal Ion Coordination In The Active Site Of Pcra Helicase.
J. Mol. Biol. V. 290 137 1999
PubMed-ID: 10388562  |  Reference-DOI: 10.1006/JMBI.1999.2873
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT HELICASE PCRA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PCRA
    Expression System Plasmid: PET22
    Expression System Taxid: 562
    Expression System Vector Type: T7 PROMOTER
    Gene: PCRA
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Strain: NCA1503

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:38 , ATP A:726BINDING SITE FOR RESIDUE MG A 725
2AC2SOFTWAREHIS A:11 , GLN A:16 , GLY A:34 , SER A:35 , GLY A:36 , LYS A:37 , ARG A:39 , TYR A:286 , ARG A:287 , GLY A:569 , MG A:725 , HOH A:736 , HOH A:851BINDING SITE FOR RESIDUE ATP A 726

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:417 -Pro A:418

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UVRD_HELICASE_ATP_BINDPS51198 UvrD-like DNA helicase ATP-binding domain profile.PCRA_GEOSE10-289  1A:10-289
2UVRD_HELICASE_CTERPS51217 UvrD-like DNA helicase C-terminal domain profile.PCRA_GEOSE290-569  1A:290-569

(-) Exons   (0, 0)

(no "Exon" information available for 1QHG)

(-) 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:622
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:651
                                    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 
           PCRA_GEOSE     1 MNFLSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDELDGTEQAAEGDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASR 651
               SCOP domains d1qhga1 A:1-318 DEXX box DNA helicase                                                                                                                                                                                                                                                                                         d1qhga2 A:319-651 DEXX box DNA helicase                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --1qhgA01 A:3-115,A:194-282 P-loop containing nucleotide  triphosphate hydrolases                                  1qhgA02 A:116-190  [code=1.10.10.160, no name def   ined]                  ---1qhgA01 A:3-115,A:194-282 P-loop containing nucleotide triphosphate hydrolases           1qhgA03 A:283-385,A:541-648 P-loop containing nucleotide triphosphate hydrolases                       -1qhgA04 A:387-538 PCRA; domain 4                                                                                                                        --1q             hgA03 A:283-385,A:541-648 P-loop containing nucleotide triphosphate hydrolases               --- CATH domains
               Pfam domains -----------UvrD-helicase-1qhgA01 A:12-275                                                                                                                                                                                                                                          ----UvrD_C-1qhgA02 A:280-622                                                                                                                                                                                                                                                                                                                               ----------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhh.............hhhhhhhhhhhhhhhh.....-..eeee.hhhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhh..---.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh....eee..hhhhh.hhhhh..hhhhhhhhhhh..............hhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhh....hhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh............------------......hhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...-------------.........hhhh.....eeee...............hhhhhhhhhhhhhhhhh....eeee.....eee..eee....hhhhhh.hhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------UVRD_HELICASE_ATP_BIND  PDB: A:10-289 UniProt: 10-289                                                                                                                                                                                                                                   UVRD_HELICASE_CTER  PDB: A:290-569 UniProt: 290-569                                                                                                                                                                                                                                     ---------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qhg A   1 MNFLSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAP-NILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKR---YYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTID------------LFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALIS-------------GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASR 651
                                    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       | -         -|      450       460       470       480       490       500       510       520       530       540 |       -     | 560       570       580       590       600       610       620       630       640       650 
                                                                                  56 |                                                                                                       164 168                                                                                                                                                                                                                                                                 428          441                                                                                                  542           556                                                                                               
                                                                                    58
   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  (1, 2)

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

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PCRA_GEOSE | P56255)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    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: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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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UniProtKB/Swiss-Prot
        PCRA_GEOSE | P56255: 1pjr 1qhh 2pjr 3pjr 5dma

(-) Related Entries Specified in the PDB File

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