6JYT,5WWP,6XEZ,6XEZ


Conserved Protein Domain Family
ZBD_cv_Nsp13-like

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cd21401: ZBD_cv_Nsp13-like 
Click on image for an interactive view with Cn3D
Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 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. This coronavirus family includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13) and belongs to helicase superfamily 1 (SF1) and to a family of nindoviral replication helicases. SARS-Nsp13 has an N-terminal CH/ZBD, a stalk domain, a 1B regulatory domain, and SF1 helicase core. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. 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 (RdRp). Structural studies of a stable SARS-CoV-2 RTC which included two molecules of Nsp13, the RdRp holoenzyme (Nsp7, two molecules of Nsp8, Nsp12), and an RNA template product, show that one Nsp13 CH/ZBD domain interacts with Nsp12, and both Nsp13-CH/ZBD domains interact with the Nsp8. This stable SARS-CoV-2 RTC suggests that the Nsp13 helicase may drive RTC backtracking, affecting proofreading and template switching.
Statistics
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PSSM-Id: 439168
Aligned: 20 rows
Threshold Bit Score: 141.37
Created: 5-Mar-2020
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
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 CClick to see conserved feature residue pattern help
Evidence:
  • Comment:named the Zn1 binding site in coronavirus SARS-Nsp13
  • Comment:zinc binding is essential for the structure and function of coronavirus SARS-Nsp13 helicase
  • Structure:6JYT: SARS-Nsp13 binds a zinc ion in the Zn1 zinc-binding site
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          #  #                 #  #                                                   
6JYT_A       3 AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNapGCDVTDVTQLYLGgXSYYCKsHKPPiS 82   Severe acute res...
AAG48591  4996 AAGLCVVCGSQTVLRCGDCLRRPMLCTKCAYDHVFGTDHKFILAITPYVCNtsGCNVNDVTKLYLGgLNYYCVdHKPHlS 5075 Human coronaviru...
Q98VG9    4953 AAGMCVVCGSQTVLRCGDCLRRPLLCTKCAYDHVMGTKHKFIMSITPYVCSfnGCNVNDVTKLFLGgLSYYCMdHKPQlS 5032 Feline infectiou...
P0C6W0    5039 SAGLCVVCSSQTVLRCGDCIRRPMLCTKCAYDHVVSTSHKFILAITPYVCCssGCGVSDVTKLYLGgLSYWCVdHKPRlS 5118 Scotophilus bat ...
P0C6Y3    4871 SCGVCVVCNSQTILRCGNCIRKPFLCCKCCYDHVMHTDHKNVLSINPYICSqpGCGEADVTKLYLGgMSYFCGnHKPKlS 4950 Avian infectious...
AHB63480  4874 ASGVCVVCNSQTVLRCGNCLRKPFLCCKCCYDHVMETEHKNVLSINPYVCSvaGCGESNVCKLFLGgMSYFCLdHKPRlA 4953 Bottlenose dolph...
ATP66783  4632 AAGLCIVCRSQTILRCGDCNRRPFLCCKCAYDHVMSTPHSFIIGITPYVCSvtDCNCSDVKKLWLSgLRYFCVdHKPSlA 4711 Shrew coronavirus
AVM87573  3054 SSGVCVVCNSQTALRCGVCVRKPFLCCRCMFEHVMQTNHKMVLSIVPYVCCvaGCGNSDVTKLYLGhMSYFCDeHKPSlS 3133 Guangdong chines...
AWV67124  4541 ASGVCVVCNSPTILRCGDCIRRPLLCCVCAYQHVTQTSHKRIIAINNYICSveNCNEDNVEKLFISgTAIYCEnHKPTlC 4620 Sparrow deltacor...
QHD43415  5325 AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNapGCDVTDVTQLYLGgMSYYCKsHKPPiS 5404 Severe acute res...
Feature 1                     
6JYT_A      83 FPLCANGQVFGLYKN 97   Severe acute respiratory syndrome-related coronavirus
AAG48591  5076 FPLCSAGNVFGLYKS 5090 Human coronavirus 229E
Q98VG9    5033 FPLCANGNVFGLYKS 5047 Feline infectious peritonitis virus (strain 79-1146)
P0C6W0    5119 FPLCSSGNVFGLYKN 5133 Scotophilus bat coronavirus 512
P0C6Y3    4951 IPLVSNGTVFGIYRA 4965 Avian infectious bronchitis virus (strain M41)
AHB63480  4954 IPLVSGGTVFGIYRA 4968 Bottlenose dolphin coronavirus HKU22
ATP66783  4712 FPICTNGFVFGLYKS 4726 Shrew coronavirus
AVM87573  3134 FPLVRGGKVFGLYMN 3148 Guangdong chinese water skink coronavirus
AWV67124  4621 IPIVANGSVFGIYRH 4635 Sparrow deltacoronavirus
QHD43415  5405 FPLCANGQVFGLYKN 5419 Severe acute respiratory syndrome coronavirus 2

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