6JYT,5WWP


Conserved Protein Domain Family
stalk_CoV_Nsp13-like

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cd21689: stalk_CoV_Nsp13-like 
stalk domain of coronavirus Nsp13 helicase and related proteins
This model represents the stalk domain of coronavirus non-structural protein 13 (Nsp13) helicase, found in the Nsp3s of alpha-, beta-, gamma-, and deltacoronaviruses, including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome coronavirus (MERS-CoV). Helicases are classified based on the arrangement of conserved motifs into six superfamilies; coronavirus helicases in this family belong to superfamily 1 (SF1). Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It consists of an N-terminal ZBD (Cys/His rich zinc-binding domain), a stalk domain, a 1B regulatory domain, and SF1 helicase core. The stalk domain lies between the ZBD domain and the 1B domain; a short loop connects the ZBD to the stalk domain. The stalk domain is comprised of three tightly-interacting alpha-helices connected to the 1B domain, transferring the effect from the ZBD domain onto the helicase core domains. The ZBD and stalk domains are critical for the helicase activity of SARS-CoV Nsp13.
Links
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Statistics
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PSSM-Id: 410205
Aligned: 59 rows
Threshold Bit Score: 84.1994
Created: 17-Aug-2020
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
key interaction
Conserved site includes 2 residues -Click on image for an interactive view with Cn3D
Feature 1:key interaction residues
Evidence:
  • Comment:based on mutagenesis studies; mutation to alanine significantly reduces helicase activity
  • Comment:these two residues are involved in hydrophilic interaction with the zinc binding domain (ZBD) and 1B domain of the helicase

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1         #                            #               
6JYT_A     101 GSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFK 148  Severe acute respiratory syndrome-related corona...
P0C6W5    5264 GSPDVADFNSLATCDWSNSKDYVLANTATERLKLFAAETLRATEENAK 5311 Rousettus bat coronavirus HKU9
P0C6W4    5500 GSPSVTEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASK 5547 Pipistrellus bat coronavirus HKU5
EZK10801   133 GSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASK 180  Escherichia coli 1-176-05_S1_C2
ASL68940  5544 GSPSVSEFNRLATCDWSESGDYILANTTTEPLKLFAAETLRATEEASK 5591 Hypsugo bat coronavirus HKU25
ADX59473  1031 GSADVADFNRLATCDWSSSSDYVLANTTTEKLKLFAAETLRATEENAK 1078 Eidolon bat coronavirus/Kenya/KY24/2006
P0C6W1    5460 GSSSIMEFNRLATCDWSDSGDYTLANTTTEPLKLFAAETLRATEEASK 5507 Bat coronavirus (BtCoV/133/2005)
P0C6W9    5396 GSPYIDDFNRIASCKWTDVDDYILANECTERLKLFAAETQKATEEAFK 5443 Bovine coronavirus Mebus
P0C6W7    5396 GSPYIDDFNRIASCKWTDVDDYILANECTERLKLFAAETQKATEEAFK 5443 Bovine enteric coronavirus (strain 98TXSF-110-ENT)
P0C6X8    5429 GSPYIEDFNKIASCKWTEVDDYVLANECTERLKLFAAETQKATEESFK 5476 Murine hepatitis virus strain 2

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