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cd00079: HELICc 
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Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Links
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Statistics
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PSSM-Id: 238034
View PSSM: cd00079
Aligned: 130 rows
Threshold Bit Score: 46.4621
Threshold Setting Gi: 2507332
Created: 1-Nov-2000
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
Hierarchy
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nucleotideATP-binding
Conserved site includes 9 residues -Click on image for an interactive view with Cn3D
Feature 1:nucleotide binding region [chemical binding site]
Evidence:
  • Structure:1A1V; Hepatitis C virus NS3 RNA helicase domain complexed with ssDNA oligonucleotide
    View structure with Cn3D
  • Citation:PMID 9493270

cd00079 is part of a hierarchy of related CD models.
Use the graphical representation to navigate this hierarchy.
cd00079 is a member of the superfamily cl19069.
cd00079:HELICc1D2M A1D9Z A312300313513873122998249909861361571GM5 A391463839146141827928539146123914611391461339146351322521343222039140142507063391401358548139140153914012391461073108713760673217439134453913437130830548590117261613080413638202250733239134342506501173095424951541A1V A1CU1 B173774167313801723776117702224951523219961285148825001125921178464912117548411728981710074250011340092017234975486694175874624952493353117008331232625865104014381723929117346666475601176015417373417308416959730465249335417310402506239135423213915469130806466042173067812644178135312125005371170186312198112732454959713478725005391723162250053817231471175447731740586550731667465975170652113516561FUU B1242172500524135243825005147293292500533250053417081521HV8 A892855311692611706338117701072953141264415111828411692281708151312218925005251706311117259654873017310061325301175401250053513487811744401D2M A1D9Z A312300313513873122998249909861361571GM5 A391463839146141827928539146123914611391461339146351322521343222039140142507063391401358548139140153914012391461073108713760673217439134453913437130830548590117261613080413638202250733239134342506501173095424951541A1V A1CU1 B173774167313801723776117702224951523219961285148825001125921178464912117548411728981710074250011340092017234975486694175874624952493353117008331232625865104014381723929117346666475601176015417373417308416959730465249335417310402506239135423213915469130806466042173067812644178135312125005371170186312198112732454959713478725005391723162250053817231471175447731740586550731667465975170652113516561FUU B1242172500524135243825005147293292500533250053417081521HV8 A89285531169261170633811770107295314126441511182841169228170815131221892500525170631111725965487301731006132530117540125005351348781174440
cd00079 Sequence Cluster
cd00079 Sequence Cluster
Sub-family Hierarchy
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CD Hierarchy
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                               ####                    ##              
1D2M_A      414 DPLVRVKPTe----nQILDL-MEGIReraa-rgeRTLVTVLTVRMAEELTSFLVe-hGIRARYLHHeld--afKRQAlir 484
1A1V_A      170 NIEEVALSTtgeipfYGKAIpLEVIKg------gRHLIFCHSKKKCDELAAKLVa-lGINAVAYYRg-----lDVSVi-- 235
gi 2506239  478 EGDNATWWNfd---pRVEWL-MGYLTshr---sqKVLVICAKAATALQLEQVLRe-rEGIRAAVFHegm-siiERDRaaa 548
gi 417308  1620 ECGIGEEDId-----KKASQ-DQNFPiqnvisqhRALIFCQLKDMLDMVENDLFkkyMPSVTYMRLdgsidprDRQKvvr 1693
gi 1723929 1290 SMDRFITESa-----KLRKL-DELLVklks-eghRVLIYFQMTKMMDLMEEYLT---YRQYNHIRLdgsskleDRRDlvh 1359
gi 1176015  594 TLETLLKTSg-----KLQIL-QKLIPplis-eghKVLIYSQFVNMLDLIEDWCD---LNSFATFRIdgsvnneTRKDqle 663
gi 1173466  388 TDQHLVDNSg-----KMVVL-DKLLMkfke-qgsRVLIFSQFSRMLDLLEDFCW---WRHYEYCRLdgstpheDRSNaie 457
gi 416959   828 EEDQFGYWKrs---gKMIVV-ESLLKiwhk-qgqRVLLFSQSRQMLDILEVFLR---AQKYTYLKMdgtttiaSRQPlit 899
gi 417373   780 RGNSDLLFRva---gKFELL-DRVLPkfka-sghRVLMFFQMTQVMDIMEDFLR---MKDLKYMRLdgstkteERTEmln 851
gi 6647560  422 TDTHLVYNSg-----KMAIL-DKLLPklqe-qgsRVLIFSQMTRMLDILEDYCH---WRNYNYCRLdgqtpheDRNRqiq 491
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                      ###                                                              
1D2M_A      485 dLRLGh---yDCLVGINLLREGLDIPeVSLVAILDadke----------------gflRSERSLIQTIGRAARNA-RGEV 544
1A1V_A      236 -PTSGd----VVVVATDALMTGFTGD-FDSVIDCNtxvtqtvdfsldptftietttlpQDAVSRTQRRGRTGRGK-PGIY 308
gi 2506239  549 wFAEEdt-gaQVLLCSEIGSEGRNFQfASHMVMFDl---------------------pFNPDLLEQRIGRLDRIGqAHDI 606
gi 417308  1694 kFNEDps-idCLLLTTKVGGLGLNLTgADTVIFVEh---------------------dWNPMNDLQAMDRAHRIGqKKVV 1751
gi 1723929 1360 dWQTNpe-ifVFLLSTRAGGLGINLTaADTVIFYDs---------------------dWNPTIDSQAMDRAHRLGqTRQV 1417
gi 1176015  664 kFNSSkdkhnIFLLSTRAAGLGINLVgADTVVLFDs---------------------dWNPQVDLQAMDRCHRIGqESPV 722
gi 1173466  458 aYNAPdskkfIFMLTTRAGGLGINLAtADVVIIYDs---------------------dWNPQSDLQAMDRAHRIGqKKQV 516
gi 416959   900 rYNEDts-ifVFLLTTRVGGLGVNLTgANRVVIYDp---------------------dWNPSTDTQARERAWRIGqKKQV 957
gi 417373   852 aFNAPdsdyfCFLLSTRAGGLGLNLQtADTVIIFDt---------------------dWNPHQDLQAQDRAHRIGqKNEV 910
gi 6647560  492 eFNMDnsakfLFMLSTRAGGLGINLAtADVVIIYDs---------------------dWNPQMDLQAMDRAHRIGqKKQV 550

                ...
Feature 1          
1D2M_A      545 WLY 547
1A1V_A      309 RFV 311
gi 2506239  607 QIH 609
gi 417308  1752 NVY 1754
gi 1723929 1418 TVY 1420
gi 1176015  723 IVY 725
gi 1173466  517 RVF 519
gi 416959   958 TVY 960
gi 417373   911 RIL 913
gi 6647560  551 RVF 553

Citing CDD
Marchler-Bauer A et al. (2013), "CDD: conserved domains and protein three-dimensional structure.", Nucleic Acids Res. 41(D1):D384-52.
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Conserved site includes 9 residues -Click on image for an interactive view with Cn3D