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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UVSW HELICASE FROM BACTERIOPHAGE T4
 
Authors :  E. A. Sickmier, S. W. White, K. N. Kreuzer
Date :  17 Nov 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bacteriophage, T4, Helicase, Uvsw, Recg, Sf2, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Sickmier, K. N. Kreuzer, S. W. White
The Crystal Structure Of The Uvsw Helicase From Bacteriophage T4.
Structure V. 12 583 2004
PubMed-ID: 15062081  |  Reference-DOI: 10.1016/J.STR.2004.02.016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA HELICASE UVSW
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET22
    Gene: UVSW, DAR
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: DAR PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1AU4Ligand/IonGOLD ION
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:67 , HOH A:295 , HOH A:354 , HOH A:414BINDING SITE FOR RESIDUE MG A 286
2AC2SOFTWAREGLN B:67 , VAL B:273 , HOH B:387 , HOH B:394BINDING SITE FOR RESIDUE MG B 288
3AC3SOFTWARECYS A:234 , HIS A:235BINDING SITE FOR RESIDUE AU A 287
4AC4SOFTWARECYS B:234 , HIS B:235BINDING SITE FOR RESIDUE AU B 283
5AC5SOFTWAREILE B:68 , CYS B:72 , ALA B:79 , HOH B:351BINDING SITE FOR RESIDUE AU B 284
6AC6SOFTWAREILE A:68 , CYS A:72 , ALA A:79BINDING SITE FOR RESIDUE AU A 285

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RIF)

(-) Exons   (0, 0)

(no "Exon" information available for 1RIF)

(-) Sequences/Alignments

Asymmetric 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:282
 aligned with UVSW_BPT4 | P20703 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:282
                                    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  
            UVSW_BPT4     1 MDIKVHFHDFSHVRIDCEESTFHELRDFFSFEADGYRFNPRFRYGNWDGRIRLLDYNRLLPFGLVGQIKKFCDNFGYKAWIDPQINEKEELSRKDFDEWLSKLEIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGKSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKP 282
               SCOP domains d1rifa_ A: DNA helicase UvsW                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------1rifA02 A:91-282 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...eeeee.hhhhhhhhhhhheee......hhhhhh.....eee......eee.hhhhhhhhhhhhh...eee.hhhhh....hhhhhhhhhhh...ee..ee...hhhhhhhhhhhhhhheeee......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...hhh.eee................eeeehhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhh.......eeeee.........hhhhhhhhhheee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rif A   1 MDIKVHFHDFSHVRIDCEESTFHELRDFFSFEADGYRFNPRFRYGNWDGRIRLLDYNRLLPFGLVGQIKKFCDNFGYKAWIDPQINEKEELSRKDFDEWLSKLEIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKP 282
                                    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  


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with UVSW_BPT4 | P20703 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:282
                                    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  
            UVSW_BPT4     1 MDIKVHFHDFSHVRIDCEESTFHELRDFFSFEADGYRFNPRFRYGNWDGRIRLLDYNRLLPFGLVGQIKKFCDNFGYKAWIDPQINEKEELSRKDFDEWLSKLEIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGKSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKP 282
               SCOP domains d1rifb_ B: DNA helicase UvsW                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------1rifB02 B:91-282 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------DEAD-1rifB01 B:116-262                                                                                                                             -------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------DEAD-1rifB02 B:116-262                                                                                                                             -------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee...eeeee.hhhhhhhhhhhheee......hhhhhh.....eee......eee.hhhhhhhhhhhhhh..eee.hhhhh....hhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhheeeee.hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh...hhh.eee................eeeeehhhhhh.hhhhhh.eeeeeee.hhhhhhhhhhhhh.......eeeeee........hhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rif B   1 MDIKVHFHDFSHVRIDCEESTFHELRDFFSFEADGYRFNPRFRYGNWDGRIRLLDYNRLLPFGLVGQIKKFCDNFGYKAWIDPQINEKEELSRKDFDEWLSKLEIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKP 282
                                    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
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UVSW_BPT4 | P20703)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.

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  1rif
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 Related Entries

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

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        UVSW_BPT4 | P20703: 2jpn 2oca

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