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539  structures 78  species 0  interactions 111  sequences 27  architectures

Family: Peptidase_C30 (PF05409)

Summary: Coronavirus endopeptidase C30

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Coronavirus endopeptidase C30 Provide feedback

This Coronavirus (CoV) domain, peptidase C30, is also known as 3C-like proteinase (3CL-pro), or CoV main protease (M-pro) domain. CoV M-pro is a dimer where each subunit is composed of three domains I, II and III [1] [2] [3]. Domains I and II consist of six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin, and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad [4] [5].

Literature references

  1. Anand K, Palm GJ, Mesters JR, Siddell SG, Ziebuhr J, Hilgenfeld R; , EMBO J 2002;21:3213-3224.: Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. PUBMED:12093723 EPMC:12093723

  2. Ziebuhr J, Snijder EJ, Gorbalenya AE; , J Gen Virol 2000;81:853-879.: Virus-encoded proteinases and proteolytic processing in the Nidovirales. PUBMED:10725411 EPMC:10725411

  3. Hegyi A, Ziebuhr J; , J Gen Virol 2002;83:595-599.: Conservation of substrate specificities among coronavirus main proteases. PUBMED:11842254 EPMC:11842254

  4. Anand K, Ziebuhr J, Wadhwani P, Mesters JR, Hilgenfeld R;, Science. 2003;300:1763-1767.: Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. PUBMED:12746549 EPMC:12746549

  5. Xue X, Yu H, Yang H, Xue F, Wu Z, Shen W, Li J, Zhou Z, Ding Y, Zhao Q, Zhang XC, Liao M, Bartlam M, Rao Z;, J Virol. 2008;82:2515-2527.: Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. PUBMED:18094151 EPMC:18094151


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008740

This group of cysteine peptidases correspond to MEROPS peptidase family C30 (clan PA(C)). These peptidases are related to serine endopeptidases of family S1 and are restricted to RNA viruses, where they are involved in viral polyprotein processing during replication [ PUBMED:12093723 , PUBMED:10725411 , PUBMED:11842254 ].

This Coronavirus (CoV) domain, peptidase C30, is also known as 3C-like proteinase (3CL-pro), or CoV main protease (M-pro) domain. CoV M-pro is a dimer where each subunit is composed of three domains I, II and III. Domains I and II consist of six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin, and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain, a globular cluster of five helices, has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad. In contrast to serine proteinases and other cysteine proteinases, which have a catalytic triad, there is no third catalytic residue present [ PUBMED:12093723 , PUBMED:12746549 , PUBMED:18094151 , PUBMED:18562531 ]. Many drugs have been developed to inhibit CoV M-pro [ PUBMED:20021285 ].

Gene Ontology

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Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(6)
Full
(111)
Representative proteomes UniProt
(13794)
RP15
(117)
RP35
(117)
RP55
(117)
RP75
(117)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(6)
Full
(111)
Representative proteomes UniProt
(13794)
RP15
(117)
RP35
(117)
RP55
(117)
RP75
(117)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(6)
Full
(111)
Representative proteomes UniProt
(13794)
RP15
(117)
RP35
(117)
RP55
(117)
RP75
(117)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Manual
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Studholme DJ , Chuguransky S
Number in seed: 6
Number in full: 111
Average length of the domain: 289.20 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 4.94 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 40.9 320.0
Noise cut-off 24.0 18.4
Model length: 288
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peptidase_C30 domain has been found. There are 539 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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