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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI UVRD
 
Authors :  S. Korolev, G. Waksman, T. M. Lohman
Date :  18 Jan 10  (Deposition) - 02 Feb 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Helicase, Sf1 Helicase, Atp-Binding, Dna Damage, Dna Repair, Dna Replication, Dna-Binding, Helicase, Hydrolase, Nucleotide-Binding, Sos Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Jia, S. Korolev, A. Niedziela-Majka, N. K. Maluf, G. H. Gauss, S. Myong, T. Ha, G. Waksman, T. M. Lohman
Rotations Of The 2B Sub-Domain Of E. Coli Uvrd Helicase/Translocase Coupled To Nucleotide And Dna Binding.
J. Mol. Biol. V. 411 633 2011
PubMed-ID: 21704638  |  Reference-DOI: 10.1016/J.JMB.2011.06.019

(-) Compounds

Molecule 1 - DNA HELICASE II
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL TRUNCATION (UNP RESIDUES 1-647)
    Gene: B3813, JW3786, MUTU, PDEB, RAD, RECL, UVRD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:31 , GLY A:32 , GLN A:251 , ARG A:284 , GLY A:564 , ARG A:605 , HOH A:856 , HOH A:951 , HOH A:1341BINDING SITE FOR RESIDUE SO4 A 1000
2AC2SOFTWARETHR A:63 , ASN A:64 , LYS A:65 , ARG A:211 , HOH A:779 , HOH A:977 , HOH A:1090 , HOH A:1227BINDING SITE FOR RESIDUE SO4 A 1001
3AC3SOFTWAREGLY A:34 , LYS A:35 , THR A:36 , ARG A:37 , ARG A:73 , HOH A:839 , HOH A:892 , HOH A:908 , HOH A:1289 , HOH A:1295BINDING SITE FOR RESIDUE SO4 A 1002
4AC4SOFTWARELYS A:135 , ARG A:460 , HOH A:875 , HOH A:1066 , HOH A:1107 , HOH A:1238 , HOH A:1338BINDING SITE FOR RESIDUE SO4 A 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:413 -Pro A:414
2Phe A:580 -Pro A:581

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UVRD_HELICASE_ATP_BINDPS51198 UvrD-like DNA helicase ATP-binding domain profile.UVRD_ECOLI8-286  1A:8-286
2UVRD_HELICASE_CTERPS51217 UvrD-like DNA helicase C-terminal domain profile.UVRD_ECOLI287-564  1A:287-564

(-) Exons   (0, 0)

(no "Exon" information available for 3LFU)

(-) 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:633
 aligned with UVRD_ECOLI | P03018 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:645
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642     
           UVRD_ECOLI     3 VSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQLRLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQSRVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEEDEDLMPLQAFLSHAALEAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSLDEGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLR 647
               SCOP domains d3lfua1 A:3-315 automated matches                                                                                                                                                                                                                                                                                        d3lfua2 A:316-647 automated matches                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------UvrD-helicase-3lfuA01 A:10-272                                                                                                                                                                                                                                         ----UvrD_C-3lfuA02 A:277-617                                                                                                                                                                                                                                                                                                                             ------------------------------ Pfam domains
         Sec.struct. author hhhhhh..hhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhh...hhh.eeeee.hhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.......----.hhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhh...eeeeeehhhhh.hhhhh...hhhhhhhhhh...eeeee......hhhhhhhhhhhhh...................eeeeeeeehhhhhhhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh-----...hhhhhhhhhhhhh-...........eeeee.hhhh...eeeeee..............--..hhhhhhhhhhhhhh.eeeeeeeeeeeeeee..eeee...hhhhhhhhhh.eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----UVRD_HELICASE_ATP_BIND  PDB: A:8-286 UniProt: 8-286                                                                                                                                                                                                                                    UVRD_HELICASE_CTER  PDB: A:287-564 UniProt: 287-564                                                                                                                                                                                                                                   ----------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lfu A   3 VSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQLRLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHI----NPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDTGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQSRVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQTDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFS-----EDLMPLQAFLSHAALE-GEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSL--GGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLR 647
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      |  - |     172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       | -   |   532        |-|      552       562       572       582   |  |592       602       612       622       632       642     
                                                                                                                                                                                      159  164                                                                                                                                                                                                                                                                                                                                                                 520   526            541 |                                        586  |                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      543                                           589
   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  (0, 0)

(no "CATH Domain" information available for 3LFU)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UVRD_ECOLI | P03018)
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:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0015616    DNA translocase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
    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:0017116    single-stranded DNA-dependent ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, in the presence of single-stranded DNA; drives the unwinding of a DNA helix.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    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: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:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    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.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
    GO:0070581    rolling circle DNA replication    A DNA-dependent DNA replication process in which a single-stranded DNA molecule is synthesized from a circular duplex template. Replication typically does not cease when one circumference has been replicated, but continues around the circumference several more times, producing a long single strand comprising multimers of the replicon.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  3lfu
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 Related Entries

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

UniProtKB/Swiss-Prot
        UVRD_ECOLI | P03018: 2is1 2is2 2is4 2is6

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