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(-) Description

Title :  E. COLI REP HELICASE/DNA COMPLEX
 
Authors :  S. Korolev, G. Waksman
Date :  30 Jun 97  (Deposition) - 09 Jul 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Complex (Helicase/Dna), Helicase, Dna Unwinding, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Korolev, J. Hsieh, G. H. Gauss, T. M. Lohman, G. Waksman
Major Domain Swiveling Revealed By The Crystal Structures Of Complexes Of E. Coli Rep Helicase Bound To Single-Stranded Dna And Adp.
Cell(Cambridge, Mass. ) V. 90 635 1997
PubMed-ID: 9288744  |  Reference-DOI: 10.1016/S0092-8674(00)80525-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - PROTEIN (ATP-DEPENDENT DNA HELICASE REP.)
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Synonym: REP HELICASE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1UAA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UVRD_HELICASE_CTERPS51217 UvrD-like DNA helicase C-terminal domain profile.REP_ECOLI281-562
 		  2A:281-562
B:281-562

(-) Exons   (0, 0)

(no "Exon" information available for 1UAA)

(-) 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:636
 aligned with REP_ECOLI | P09980 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:639
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631         
            REP_ECOLI     2 RLNPGQQQAVEFVTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDTDQLALLKELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCYGLYDAHLKACNVLDFDDLILLPTLLLQRNEEVRKRWQNKIRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALKVIKLEQNYRSSGRILKAANILIANNPHVFEKRLFSELGYGAELKVLSANNEEHEAERVTGELIAHHFVNKTQYKDYAILYRGNHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPKREIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRLAEREPIAAVRDLIHGMDYESWLYETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMTLTQVVTRFTLRDMMERGESEEELDQVQLMTLHASKGLEFPYVYMVGMEEGFLPHQSSIDEDNIDEERRLAYVGITRAQKELTFTLCKERRQYGELVRPEPSRFLLELPQDDLIW 640
               SCOP domains d1uaaa1 A:2-307 DEXX box DNA helicase                                                                                                                                                                                                                                                                             d1uaaa2 A:308-640 DEXX box DNA helicase                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1uaaA01 A:2-107,A:185-273 P-loop containing nucleotide triphosphate hydrolases                            1uaaA02 A:108-181  [code=1.10.10.160, no name defined]                    ---1uaaA01 A:2-107,A:185-273 P-loop containing nucleotide triphosphate hydrolases           1uaaA03 A:274-376,A:542-639 P-loop containing nucleotide triphosphate hydrolases                       -1uaaA04 A:378-539 PCRA; domain 4                                                                                                                                  --1   uaaA03 A:274-376,A:542-639 P-loop containing nucleotide triphosphate hydrolases               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh....eeee.......hhhhhhhhhhhhhhhh...hhheeeee..hhhhhhhhhhhhhh.........eeeehhhhhhhhhhhhhhh...........hhhhhhhhhhhh.......hhhhhhhhhhhhhhh.......hhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhh....eeee..hhh..hhhhhhhhhhh.....eeee..hhh...hhh...hhhhhhhhhh....eee.........hhhhhhhhhhhhh...................eeee...hhhhhhhhhhhhhhhhhhh...hhheeeee...hhh..hhhhhhhh...eee.....hhh.hhhhhhhhhhhhhh....hhhhhhh.........hhhhhhhhhhhhh....hhhhhh...hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh......---......eeeee..........eeee..........hhhhhh...hhhhhhhhhhhhh...eeeeee................hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UVRD_HELICASE_CTER  PDB: A:281-562 UniProt: 281-562                                                                                                                                                                                                                                       ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uaa A   2 RLNPGQQQAVEFVTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDTDQLALLKELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCYGLYDAHLKACNVLDFDDLILLPTLLLQANEEVRKRWQNKIRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALKVIKLEQNYRSSGRILKAANILIANNPHVFEKRLFSELGYGAELKVLSANNEEHEAERVTGELIAHHFVNKTQYKDYAILYRGNHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPKREIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRLAEREPIAAVRDLIHGMDYESWLYETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMTLTQVVTRFTLRDMMER---EEELDQVQLMTLHASKGLEFPYVYMVGMEEGFLPHQSSIDEDNIDEERRLAYVGITRAQKELTFTLCKERRQYGELVRPEPSRFLLELPQDDLIW 640
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541|   |  551       561       571       581       591       601       611       621       631         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      542 546                                                                                              


Chain B from PDB  Type:PROTEIN  Length:633
 aligned with REP_ECOLI | P09980 from UniProtKB/Swiss-Prot  Length:673

    Alignment length:641
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641 
            REP_ECOLI     2 RLNPGQQQAVEFVTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDTDQLALLKELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCYGLYDAHLKACNVLDFDDLILLPTLLLQRNEEVRKRWQNKIRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALKVIKLEQNYRSSGRILKAANILIANNPHVFEKRLFSELGYGAELKVLSANNEEHEAERVTGELIAHHFVNKTQYKDYAILYRGNHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPKREIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRLAEREPIAAVRDLIHGMDYESWLYETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMTLTQVVTRFTLRDMMERGESEEELDQVQLMTLHASKGLEFPYVYMVGMEEGFLPHQSSIDEDNIDEERRLAYVGITRAQKELTFTLCKERRQYGELVRPEPSRFLLELPQDDLIWEQ 642
               SCOP domains d1uaab1 B:2-307 DEXX box DNA helicase                                                                                                                                                                                                                                                                             d1uaab2 B:308-642 DEXX box DNA helicase                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1uaaB01 B:2-107,B:185-273 P-loop containing nucleotide triphosphate hydrolases                            1uaaB02 B:108-181  [code=1.10.10.160, no name defined]                    ---1uaaB01 B:2-107,B:185-273 P-loop containing nucleotide triphosphate hydrolases           1uaaB03 B:274-376,B:533-640 P-loop containing nucleotide triphosphate hydrolases                       -1uaaB04 B:378-530 PCRA; domain 4                                                                                                                         --1uaaB0        3 B:274-376,B:533-640 P-loop containing nucleotide triphosphate hydrolases                    -- CATH domains
           Pfam domains (1) -UvrD-helicase-1uaaB01 B:3-266                                                                                                                                                                                                                                           ----UvrD_C-1uaaB03 B:271-614                                                                                                                                                                                                                                                                                                                                ---------------------------- Pfam domains (1)
           Pfam domains (2) -UvrD-helicase-1uaaB02 B:3-266                                                                                                                                                                                                                                           ----UvrD_C-1uaaB04 B:271-614                                                                                                                                                                                                                                                                                                                                ---------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhh.....eeeee.....hhhhhhhhhhhhhhh....hhheeee...hhhhhhhhhhhhhh.............hhhhhhhhhhhhh..............hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhh....eeee..hhh..hhhhhhhhhh......eeeee.hhh..hhhh...hhhhhhhhhh....eeeee.......hhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhhhhhhhhh...hhheeeee...hhhhhhhhhhhhh...........hhh.hhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhh....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.--------......eeeehhhh......eeee..........hhhhhh...hhhhhhhhhhhhh...eeeeeee...............hhhhh..hhheee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UVRD_HELICASE_CTER  PDB: B:281-562 UniProt: 281-562                                                                                                                                                                                                                                       -------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uaa B   2 RLNPGQQQAVEFVTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLGRKEARGLMISTFHTLGLDIIKREYAALGMKANFSLFDDTDQLALLKELTEGLIEDDKVLLQQLISTISNWKNDLKTPSQAAASAIGERDRIFAHCYGLYDAHLKACNVLDFDDLILLPTLLLQANEEVRKRWQNKIRYLLVDEYQDTNTSQYELVKLLVGSRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFPALKVIKLEQNYRSSGRILKAANILIANNPHVFEKRLFSELGYGAELKVLSANNEEHEAERVTGELIAHHFVNKTQYKDYAILYRGNHQSRVFEKFLMQNRIPYKISGGTSFFSRPEIKDLLAYLRVLTNPDDDSAFLRIVNTPKREIGPATLKKLGEWAMTRNKSMFTASFDMGLSQTLSGRGYEALTRFTHWLAEIQRLAEREPIAAVRDLIHGMDYESWLYETSPSPKAAEMRMKNVNQLFSWMTEMLEGSELDEPMTLTQVVTRFTLRD--------EELDQVQLMTLHASKGLEFPYVYMVGMEEGFLPHQSSIDEDNIDEERRLAYVGITRAQKELTFTLCKERRQYGELVRPEPSRFLLELPQDDLIWEQ 642
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531      |  -     | 551       561       571       581       591       601       611       621       631       641 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  538      547                                                                                               


Chain C from PDB  Type:DNA  Length:16
                                                
                 1uaa C   1 TTTTTTTTTTTTTTTT  16
                                    10
   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, 4)

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

(-) CATH Domains  (3, 8)

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

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (REP_ECOLI | P09980)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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.
    GO:0044787    bacterial-type DNA replication    The DNA-dependent DNA replication, exemplified by prokaryotes, that occurs as part of the cell cycle. Prokaryotic DNA replication is bi-directional and originates at a single origin of replication on the circular genome.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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