5WWP,2WJV,2IYK,6JYT,4N0N


Conserved Protein Domain Family
ZBD_UPF1_nv_SF1_Hel-like
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cd21343: ZBD_UPF1_nv_SF1_Hel-like 
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Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, 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. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10, as well as eukaryotic UPF1 helicase. 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 CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. UPF1, SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core.
Links
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Statistics
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PSSM-Id: 439166
Aligned: 8 rows
Threshold Bit Score: 55.1921
Created: 13-Oct-2021
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 [CH]Click to see conserved feature residue pattern help
Evidence:
  • Comment:named the Zn1 binding site in human UPF1, SARS-Nsp13 and EAV-Nsp10
  • Comment:zinc ions are important for UPF1, SARS-Nsp13 and EAV-Nsp10 structure and function
  • Structure:2IYK: human UPF1 binds a zinc ion in the Zn1 zinc-binding site
  • Structure:6JYT: SARS-Nsp13 binds a zinc ion in the Zn1 zinc-binding site
Scroll to Sequence Alignment Display
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1          #  #                       #         #                                         
5WWP_B          6 SCVVCHSQt---sLRCGtCi---rRPFLCc-------KCCYDHViatPHKMVLsvs-------pyvCnapgCgvSDVtkl 65   Human betacor...
2WJV_A          8 ACSYCGIHdpacvVYCNtS-----KKWFCngrgntsgSHIVNHLvraKCKEVTlhkdgplgetvleCy--nCgcRNVfll 80   human
2IYK_A         12 ACSYCGIHdpacvVYCNtS-----KKWFCngrgntsgSHIVNHLvraKCKEVTlhkdgplgetvleCy--nCgcRNVfll 84   human
6JYT_A          6 ACVLCNSQt---sLRCGaCi---rRPFLCc-------KCCYDHVistSHKLVLsvn-------pyvCnapgCdvTDVtql 65   Severe acute ...
4N0N_A         24 VCTVCGAAp----VAKSaC-----GGWFCg-------NCVPYHAg-hCHTTSLfa----------nC----G--HDImyr 70   Equine arteri...
YP_001661452 5242 ICFACGGHg---qFECYtCasngyPFTFCng-----sTCLRTHFtecEHYSYSlasrk---ryiiqCa--dCeeMDIrkm 5308 Gill-associat...
AGL73177     1090 NCYVCGENa---yLTCAtC-----ERAFCnsadtnhgSHIEQHLqysGHTCLYlnck------tvkCq--hCftNDInll 1153 Bontang virus
AXP11707     6012 QCYCCQNPt---vSVCTsCp---vAYPLCc-------YCACEHYnqtHHKVTHlp----------tCavvgCgeSDPelm 6068 Bellinger Riv...

Feature 1                            
5WWP_B         66 yl------ggmsyFCVd-H 77   Human betacoronavirus 2c EMC/2012
2WJV_A         81 gfipakadsvvvlLCRqpC 99   human
2IYK_A         85 gfipakadsvvvlLCRqpC 103  human
6JYT_A         66 yl------ggxsyYCKs-H 77   Severe acute respiratory syndrome-related coronavirus
4N0N_A         71 s--------tyctMCEg-S 80   Equine arteritis virus Bucyrus
YP_001661452 5309 yv-------nndfRCAr-H 5319 Gill-associated virus
AGL73177     1154 yt------tgrehFCVs-H 1165 Bontang virus
AXP11707     6069 nfal--dngnftiRCNd-H 6084 Bellinger River virus

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