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(-) Description

Title :  CRYSTAL STRUCTURE OF THE T4 PHAGE SF1B HELICASE DDA
 
Authors :  X. He, M. K. Yun, C. W. Pemble Iv, K. N. Kreuzer, K. D. Raney, S. W. White
Date :  18 Nov 11  (Deposition) - 20 Jun 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Reca-Like Domain, Sh3 Domain, Pin-Tower Interface, Coupling Atp Hydrolysis To Dna Unwinding, Ssdna, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. He, A. K. Byrd, M. K. Yun, C. W. Pemble, D. Harrison, L. Yeruva, C. Dahl K. N. Kreuzer, K. D. Raney, S. W. White
The T4 Phage Sf1B Helicase Dda Is Structurally Optimized To Perform Dna Strand Separation.
Structure V. 20 1189 2012
PubMed-ID: 22658750  |  Reference-DOI: 10.1016/J.STR.2012.04.013

(-) Compounds

Molecule 1 - ATP-DEPENDENT DNA HELICASE DDA
    ChainsA, B, C
    EC Number3.6.4.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDDA, SUD
    MutationYES
    Organism ScientificENTEROBACTERIA PHAGE T4
    Organism Taxid10665
    SynonymSF1B HELICASE DDA
 
Molecule 2 - 5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'
    ChainsD, E, F
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A  D  
Biological Unit 2 (1x) B  E 
Biological Unit 3 (1x)  C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 21)

Asymmetric Unit (1, 21)
No.NameCountTypeFull Name
1MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3UPU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UPU)

(-) Exons   (0, 0)

(no "Exon" information available for 3UPU)

(-) 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:439
 aligned with DDA_BPT4 | P32270 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:439
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
             DDA_BPT4     1 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGKTTLTKFIIEALISTGGTGIILAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIPPWCTIIGIGDNKQIRPVEPGENTAYISPFFTHKDFYQCELTEVKRSNAPIIDVATDVRNGKWNYDKVVDGHGVRGFTGDTALRDFMVNYFSIVKSLDDLFENRVMAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVMQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFVKARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLAKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGMSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 439
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh..eeehhhhhheeeee....eeeee..........eeee.hhhhhhhhhhhhhhhhh....eeeeee.................hhhhh...eeeee........hhhhhhhhhhhh......eee..eeeee.....hhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhhhh..........eeee...eeeeeee..eeeeeeee....eeeeeeeeeeeeee........eeeeeeeeeeee.......eeeeee..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh....eee..eee.hhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3upu A   1 mTFDDLTEGQKNAFNIVmKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSmYDRKLFKILLSTIPPWCTIIGIGDNKQIRPVDPGENTAYISPFFTHKDFYQCELTEVKRSNAPIIDVATDVRNGKWIYDKVVDGHGVRGFTGDTALRDFmVNYFSIVKSLDDLFENRVmAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVmQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFVKARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLGKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGmSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 439
                            |       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       290       300       310       320       330       340       350       360       370       380       390       400|      410       420       430         
                            |               18-MSE                                                                                              119-MSE                                                                                             219-MSE            238-MSE                          271-MSE                                                                                                                           401-MSE                                  
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:439
 aligned with DDA_BPT4 | P32270 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:439
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
             DDA_BPT4     1 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGKTTLTKFIIEALISTGGTGIILAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIPPWCTIIGIGDNKQIRPVEPGENTAYISPFFTHKDFYQCELTEVKRSNAPIIDVATDVRNGKWNYDKVVDGHGVRGFTGDTALRDFMVNYFSIVKSLDDLFENRVMAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVMQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFVKARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLAKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGMSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 439
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh...eehhhhh.eeeee....eeeee..........eeee.hhhhhhhhhhhhhhh......eeeeee.................hhhhh...ee...........hhhhhhhhhhhh......eee..eeeee.....hhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhhhh..........eeee...eeeeeee..eeeeeeee....eeeeeeeeeeeeee........eeeeeeeeeeee.......eeeeee..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh.ee.eee..eee.hhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3upu B   1 mTFDDLTEGQKNAFNIVmKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSmYDRKLFKILLSTIPPWCTIIGIGDNKQIRPVDPGENTAYISPFFTHKDFYQCELTEVKRSNAPIIDVATDVRNGKWIYDKVVDGHGVRGFTGDTALRDFmVNYFSIVKSLDDLFENRVmAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVmQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFVKARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLGKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGmSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 439
                            |       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       290       300       310       320       330       340       350       360       370       380       390       400|      410       420       430         
                            1-MSE           18-MSE                                                                                              119-MSE                                                                                             219-MSE            238-MSE                          271-MSE                                                                                                                           401-MSE                                  

Chain C from PDB  Type:PROTEIN  Length:439
 aligned with DDA_BPT4 | P32270 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:439
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
             DDA_BPT4     1 MTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGKTTLTKFIIEALISTGGTGIILAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSMYDRKLFKILLSTIPPWCTIIGIGDNKQIRPVEPGENTAYISPFFTHKDFYQCELTEVKRSNAPIIDVATDVRNGKWNYDKVVDGHGVRGFTGDTALRDFMVNYFSIVKSLDDLFENRVMAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVMQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFVKARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLAKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGMSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 439
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeehhhhhheeeee....eeeee..........eeeee.hhhhhhhhhhhhhhhh....eeeeee.................hhhhh...eeeee........hhhhhhhhhhhh......eee..eeeee.....hhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhhhh..........eeee...eeeeeee..eeeeeeee....eeeeeeeeeeeeee........eeeeeeeeeeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.ee.eee..eee.hhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3upu C   1 mTFDDLTEGQKNAFNIVmKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLSGKEASTIHSILKINPVTYEENVLFEQKEVPDLAKCRVLICDEVSmYDRKLFKILLSTIPPWCTIIGIGDNKQIRPVDPGENTAYISPFFTHKDFYQCELTEVKRSNAPIIDVATDVRNGKWIYDKVVDGHGVRGFTGDTALRDFmVNYFSIVKSLDDLFENRVmAFTNKSVDKLNSIIRKKIFETDKDFIVGEIIVmQEPLFKTYKIDGKPVSEIIFNNGQLVRIIEAEYTSTFVKARGVPGEYLIRHWDLTVETYGDDEYYREKIKIISSDEELYKFNLFLGKTAETYKNWNKGGKAPWSDFWDAKSQFSKVKALPASTFHKAQGmSVDRAFIYTPCIHYADVELAQQLLYVGVTRGRYDVFYV 439
                            |       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       290       300       310       320       330       340       350       360       370       380       390       400|      410       420       430         
                            1-MSE           18-MSE                                                                                              119-MSE                                                                                             219-MSE            238-MSE                          271-MSE                                                                                                                           401-MSE                                  

Chain D from PDB  Type:DNA  Length:8
                                        
                 3upu D 600 TTTTTTTT 607

Chain E from PDB  Type:DNA  Length:8
                                        
                 3upu E 600 TTTTTTTT 607

Chain F from PDB  Type:DNA  Length:8
                                        
                 3upu F 600 TTTTTTTT 607

   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3UPU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UPU)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DDA_BPT4 | P32270)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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.

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