2WJV,2IYK,2XZL


Conserved Protein Domain Family
ZBD_UPF1-like
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cd21400: ZBD_UPF1-like 
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Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins
Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core.
Links
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Statistics
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PSSM-Id: 439167
Aligned: 174 rows
Threshold Bit Score: 79.2134
Created: 26-Feb-2020
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
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Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1: Zn binding site [ion binding site], 4 residue positions
Conserved feature residue pattern:C C C HClick to see conserved feature residue pattern help
Evidence:
  • Comment:named the Zn1 binding site in human UPF1
  • Comment:zinc ions are important for UPF1 structure and function
  • Structure:2IYK: human UPF1 binds a zinc ion in the Zn1 zinc-binding site
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1          #  #                     #                #                                    
2WJV_A          8 ACSYCGIHdp-aCVVYCNt--SKKWFCNGRgnt-------sgSHIVNHLVraKCKEVTLHk----dGPLGETVLECYn-- 71   human
2IYK_A         12 ACSYCGIHdp-aCVVYCNt--SKKWFCNGRgnt-------sgSHIVNHLVraKCKEVTLHk----dGPLGETVLECYn-- 75   human
OMJ85788       49 ACDYCGETse-nTLFRCAeaeCGRWFCNNSfike-----tkaSHLIFHLNtfNHKKVEVHe----fSQLGPIVFECIs-- 116  Stentor coeru...
OQV18741      127 CCSYCGQDes-aTMVKCMd--CNKWFCNGTsetktrngtqkeSHIIIHLRasKHHRSIAVy----dTSDQLTAIRCTgpd 199  Hypsibius duj...
XP_009497545   92 ACGMCQSTdp-eCLGQCGd--CRRWFCNGTwnp------aqpSHLVWHLAqkKHRSLRLHr----gHPLGRQPIECTv-- 156  Fonticula alba
OAO17633       25 CCQYCGNGps-vCLAKCLt--CGKFFCNGTglk-------egSHLSVHMRvsKHKSFQVYs----nTFQPGMVPKCKv-- 88   Blastocystis ...
GAU88968        5 QCGFCQSKdt-gCLVQCVqedCNLWFCNGNseees--vqhkeSHILSHLHmaDHRKIAVRq----kNQPKVFSVICHk-- 75   Ramazzottius ...
OQV17667        4 GCSFCGQAhs-eFLVKCVkngCGKWFCNGStdsngq-sgpkeSHIISHLRisRHREIAVPscptetGDYQLFYFCCMl-- 79   Hypsibius duj...
XP_001707280    3 PCALCGSLa--ePLVRCGa--CREVYCNNFdh--------ktSHIVRHLQltGHDHIEPVs----eFYIPSDVLYCNd-- 64   Giardia lambl...
TNJ27086        6 RCETCGADdlatTLIRCRn--CGAVHCNRPea--------tpSHIIGHLQatGHTEIAPIt----tCHLQEDDFVCTs-- 69   Giardia muris

Feature 1                                                                                 
2WJV_A         72 CGCRNVFLLGFIPaka-----dsVVVLLCRqPCAsqsslkdinWDSSQ-------WQPLIQ---DRCFLSWL 128  human
2IYK_A         76 CGCRNVFLLGFIPaka-----dsVVVLLCRqPCAsqsslkdinWDSSQ-------WQPLIQ---DRCFLSWL 132  human
OMJ85788      117 CKTSNIFSLGYIPa---------FDAIYCRvPCLnd-----feIEISA-------WMPLVV---DKALALDD 164  Stentor coeruleus
OQV18741      200 CDETNCFDMGTVVdpd----kslLACCLCR-PCAiqm----kkFGSSD-------WLILVD---CHNPALKC 252  Hypsibius dujardini
XP_009497545  157 CQAPDIWRLSVSTsl-------gRGPVVCCePCIgeyq--aadWPMSW-------SAVVGPraiAGELLPSR 212  Fonticula alba
OAO17633       89 CGCTNVFDLRLLKdaq-----grILGLVCLeKCIs-------sMKLTNpayanlsYEPVIV---KEGICPEV 145  Blastocystis sp. ATCC...
GAU88968       76 CDEPNVFDLYEQLktrkttsnvvPGVVFCRtCALsq-----ksYNAAD-------WKPVID---CHHDILAC 132  Ramazzottius varieorn...
OQV17667       80 CDRNDSFDMGMETagd----grnASKHLCRqDALel------gKFSREg-----sWVPFVD---VHHRSLKC 133  Hypsibius dujardini
XP_001707280   65 CETKGITSLGFLPtka-----daCSGIICCvNCRmyh---dqtHDTSA-------WRPIIS---THIDSRFF 118  Giardia lamblia ATCC ...
TNJ27086       70 CGERTIWMLGYLPlle-----neCQGFICCaACStry---seqCAVDQ-------WRKLAD---TCISPFLF 123  Giardia muris

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