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(-) Description

Title :  HELICASE SUBSTRATE COMPLEX
 
Authors :  S. S. Velankar, P. Soultanas, M. S. Dillingham, H. S. Subramanya, D. B. W
Date :  12 Mar 99  (Deposition) - 08 Apr 99  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,Y,Z
Keywords :  Helicase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Velankar, P. Soultanas, M. S. Dillingham, H. S. Subramanya, D. B. Wigley
Crystal Structures Of Complexes Of Pcra Dna Helicase With A Dna Substrate Indicate An Inchworm Mechanism
Cell(Cambridge, Mass. ) V. 97 75 1999
PubMed-ID: 10199404  |  Reference-DOI: 10.1016/S0092-8674(00)80716-3

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*TP*TP*T)-3'
    Chains: Y
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*C)-3'
    Chains: Z
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - HELICASE PCRA
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AYZ

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 , GLN A:16 , ALA A:33 , SER A:35 , GLY A:36 , LYS A:37 , THR A:38 , ARG A:39 , GLN A:254 , TYR A:286 , ARG A:287 , GLU A:571 , ARG A:610BINDING SITE FOR RESIDUE ATP A 725

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PJR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PJR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PJR)

(-) 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 3PJR)

(-) 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:646
 aligned with PCRA_GEOSE | P56255 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:649
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643         
           PCRA_GEOSE     4 LSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDELDGTEQAAEGDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASRR 652
               SCOP domains d3pjra1 A:4-318 DEXX box DNA helicase                                                                                                                                                                                                                                                                                      d3pjra2 A:319-652 DEXX box DNA helicase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3pjrA01 A:4-112,A:193-282 P-loop containing nucleotide triphosphate hydrolases                               3pjrA02 A:113-192  [code=1.10.10.160, no name defined]                          3pjrA01 A:4-112,A:193-282 P-loop containing nucleotide triphosphate hydrolases            3pjrA03 A:283-385,A:550-652 P-loop containing nucleotide triphosphate hydrolases                       3pjrA04 A:386-546 PCRA; domain 4                                                                                                                                 ---3pjrA03 A:283-385,A:550-652 P-loop containing nucleotide triphosphate hydrolases                        CATH domains
               Pfam domains --------UvrD-helicase-3pjrA01 A:12-275                                                                                                                                                                                                                                          ----UvrD_C-3pjrA02 A:280-622                                                                                                                                                                                                                                                                                                                               ------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh...hhh.eeeee.hhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhh.........eeehhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh......eee.hhhhh.hhhhh.......hhhhhh...eeee.......hhhhhhhhhhhh........................ee.hhhhhhhhhhhhhhhhhh....hhh.eeeee.....hhhhhhhhhhh...ee.........hhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....---.........eeeee.hhhh...eeeeee................hhhhhhhhhhhhhhhhheeeeee..ee.eeee..eeee...hhhhhhh........... 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
                 3pjr A   4 LSEQLLAHLNKEQQEAVRTTEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLGGAAEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTDQLSVMKTILKEKNIDPKKFEPRTILGTISAAKNELLPPEQFAKRASTYYEKVVSDVYQEYQQRLLRNHSLDFDDLIMTTIQLFDRVPDVLHYYQYKFQYIHIDEYQDTNRAQYTLVKKLAERFQNICAVGDADQSIYRWRGADIQNILSFERDYPNAKVILLEQNYRSTKRILQAANEVIEHNVNRKPKRIWTENPEGKPILYYEAMNEADEAQFVAGRIREAVERGERRYRDFAVLYRTNAQSRVMEEMLLKANIPYQIVGGLKFYDRKEIKDILAYLRVIANPDDDLSLLRIINVPKRGIGASTIDKLVRYAADHELSLFEALGELEMIGLGAKAAGALAAFRSQLEQWTQLQEYVSVTELVEEVLDKSGYREMLKAERTIEAQSRLENLDEFLSVTKHFENVSDDKSLIAFLTDLALISDLDE---TEQAAEGDAVMLMTLHAAKGLEFPVVFLIGMEEGIFPHNRSLEDDDEMEEERRLAYVGITRAEEELVLTSAQMRTLFGNIQMDPPSRFLNEIPAHLLETASRR 652
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543  |   |553       563       573       583       593       603       613       623       633       643         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        546 550                                                                                                      


Chain Y from PDB  Type:DNA  Length:15
                                               
                 3pjr Y   1 GCAGTGCTCGTTTTT  15
                                    10     


Chain Z from PDB  Type:DNA  Length:10
                                          
                 3pjr Z  25 CGAGCACTGC  34
                                    34
   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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  3pjr
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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