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(-) Description

Title :  STRUCTURE OF DNA HELICASE 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,B,C,D
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 - PROTEIN (PCRA (SUBUNIT))
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GenePCRA
    Expression System PlasmidPET22
    Expression System Taxid562
    Expression System Vector TypeT7 PROMOTER
    GenePCRA
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    StrainNCA1503
 
Molecule 2 - PROTEIN (PCRA (SUBUNIT))
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GenePCRA
    Expression System PlasmidPET22
    Expression System Taxid562
    Expression System Vector TypeT7 PROMOTER
    GenePCRA
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    StrainNCA1503
 
Molecule 3 - PROTEIN (PCRA (SUBUNIT))
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GenePCRA
    Expression System PlasmidPET22
    Expression System Taxid562
    Expression System Vector TypeT7 PROMOTER
    GenePCRA
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    StrainNCA1503
 
Molecule 4 - PROTEIN (PCRA (SUBUNIT))
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GenePCRA
    Expression System PlasmidPET22
    Expression System Taxid562
    Expression System Vector TypeT7 PROMOTER
    GenePCRA
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    StrainNCA1503

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , LEU A:12 , ASN A:13 , GLN A:16 , ALA A:33 , GLY A:34 , GLY A:36 , THR A:38 , ARG A:39 , GLN B:254 , TYR B:286 , ARG B:287 , HOH B:791 , GLY D:569 , GLU D:571 , ARG D:610BINDING SITE FOR RESIDUE ATP A 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val B:417 -Pro B:418
2Phe D:585 -Pro D:586

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:10-164
2UVRD_HELICASE_CTERPS51217 UvrD-like DNA helicase C-terminal domain profile.PCRA_GEOSE290-569  1B:290-428

(-) Exons   (0, 0)

(no "Exon" information available for 1QHH)

(-) 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:164
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           PCRA_GEOSE     1 MNFLSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKR 164
               SCOP domains d1qhh.1 A:,B:,C:,D: DEXX box DNA helicase                                                                                                                            SCOP domains
               CATH domains 1qhhA00 A:1-164 P-loop containing nucleotide triphosphate hydrolases                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....hhhhhhhh...............hhhhhhhhhhhhhh.....hhh.eeee..hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh............hhhhhhhhhhh..........hhhhhhhhhhhhhh...hhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------UVRD_HELICASE_ATP_BIND  PDB: A:10-164 UniProt: 10-289                                                                                                       PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qhh A   1 MNFLSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKR 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:261
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427 
           PCRA_GEOSE   168 YYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTID 428
               SCOP domains d1qhh.1 A:,B:,C:,D: DEXX box DNA helicase                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) UvrD-helicase-1qhhB01 B:168-275                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) UvrD-helicase-1qhhB02 B:168-275                                                                             --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhh...eee..hhh..hhhhhhhhhhh.....eee...hhh...hhh...hhhhhhhhhh................hhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhh......hhh.......hhhhhhhhhhhhh............hhh.hhhhhhhhhhhhhh....hhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UVRD_HELICASE_ATP_BIND  PDB: - UniProt: 10-289                                                                            UVRD_HELICASE_CTER  PDB: B:290-428 UniProt: 290-569                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qhh B 168 YYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTID 428
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427 

Chain C from PDB  Type:PROTEIN  Length:102
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:102
                                   450       460       470       480       490       500       510       520       530       540  
           PCRA_GEOSE   441 LFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALIS 542
               SCOP domains d1qhh.1 A:,B:,C:,D: DEXX box DNA helicase                                                              SCOP domains
               CATH domains 1qhhC00 C:441-542 PCRA; domain 4                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.hhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE UVRD_HELICASE_CTER  PDB: - UniProt: 290-569                                                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1qhh C 441 LFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALIS 542
                                   450       460       470       480       490       500       510       520       530       540  

Chain D from PDB  Type:PROTEIN  Length:96
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:96
                                   565       575       585       595       605       615       625       635       645      
           PCRA_GEOSE   556 GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASR 651
               SCOP domains d1qhh.1 A:,B:,C:,D: DEXX box DNA helicase                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) UvrD_C-1qhhD01 D:556-622                                           ----------------------------- Pfam domains (1)
           Pfam domains (2) UvrD_C-1qhhD02 D:556-622                                           ----------------------------- Pfam domains (2)
           Pfam domains (3) UvrD_C-1qhhD03 D:556-622                                           ----------------------------- Pfam domains (3)
         Sec.struct. author ........hhhh......eeee..........hhhhh.hhhhhhhhhhhhhhhhh...eeee.....eee..eee.....hhhh...hhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE UVRD_HELICASE_---------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1qhh D 556 GDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASR 651
                                   565       575       585       595       605       615       625       635       645      

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 5)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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

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

UniProtKB/Swiss-Prot
        PCRA_GEOSE | P562551pjr 1qhg 2pjr 3pjr 5dma

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QHH)