Conserved Protein Domain Family

cd00394: Clp_protease_like 
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Caseinolytic protease (ClpP) is an ATP-dependent protease
Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad.
PSSM-Id: 132923
Aligned: 9 rows
Threshold Bit Score: 133.672
Created: 6-Mar-2002
Updated: 2-Oct-2020
Aligned Rows:
active site
Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
  • Structure:1TYF_A: E. coli Clp Protease (ClpP) active site triad: Ser, His, Asp
    View structure with Cn3D
  • Citation:PMID 9390554
  • Structure:3BPP: Pyrococcus horikoshii 1510-N membrane protease K138A mutant specific for a stomatin homolog
    View structure with Cn3D
  • Comment:The N- and C-terminal halves of SppA in E. coli are tandem repeats and the Ser/Lys dyad is arranged such that the nucleophile Ser is located in the C-terminal half whereas the general base Lys is located in the N-terminal half.
  • Structure:3BEZ: E. coli Signal peptide peptidase A (SppA)
    View structure with Cn3D

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                     
1TYF_A     28 VIFLTGqved-------------------------hmaNLIVAQMLFLEAenpekDIYLYINSpgg-vitAGMSIYDTMQ 81  Escherichia coli
3BEZ_A    305 VVFANGaixdgee------------------tqgnvggDTTAAQIRDARLdpkvkAIVLRVNSpgg-svtASEVIRAELA 365 Escherichia coli
3BEZ_A     35 LLDISGvivdkpdssqrfsklsrqllgassdrlqenslFDIVNTIRQAKDdrnitGIVXDLKNfaggdqpSXQYIGKALK 114 Escherichia coli
3BPP_A     12 VAQIKGqits-------------------------ytyDQFDRYITIAEQdn-aeAIIIELDTpgg-radAMMNIVQRIQ 64  Pyrococcus horikoshii
NP_242222  41 YIPVEQever-------------------------gleAFLQRSLDSAVEeg-adHIVLEINTpgg-rvdAAGNMARALR 93  Bacillus haloduran...
2DEO_A     12 VAQIKGqits-------------------------ytyDQFDRYITIAEQdn-aeAIIIELDTpgg-radAXXNIVQRIQ 64  Pyrococcus horikoshii
ABX56715   60 IIHVNGvisryanlf--------------havcggvstEVLAKEFNAALNessvkAVILNVDSpgg-easGIHELSEMIH 124 Vibrio shilonii
3BF0_A    305 VVFANGaimdgee------------------tqgnvggDTTAAQIRDARLdpkvkAIVLRVNSpgg-svtASEVIRAELA 365 Escherichia coli
1Y7O_A     47 IIXLTGpved-------------------------nxaNSVIAQLLFLDAqdstkDIYLYVNTpgg-svsAGLAIVDTXN 100 Streptococcus pneu...
Feature 1                          #                                                          
1TYF_A     82 Fik---pDVSTICm---gQAASMGAFLLTAgakgkRFCLPNSRVMihqPLGgyqgqa----------------------- 132 Escherichia coli
3BEZ_A    366 AaraagkPVVVSXg---gXAASGGYWISTPan--yIVANPSTLTGsigIFGvittvensldsigvhtdgvst---splad 437 Escherichia coli
3BEZ_A    115 EfrdsgkPVYAVGe----NYSQGQYYLASFan--kIWLSPQGVVDlhgFATnglyykslldklkvsthvfrvgtyksave 188 Escherichia coli
3BPP_A     65 Qsk---iPVIIYVyppgaSAASAGTYIALGsh--lIAMAPGTSIGacrPILgysqng----------------------- 116 Pyrococcus horikoshii
NP_242222  94 Etd---iPITAYVi---dQALSAGAYIALNad--eIVMAPGSTMGsaaVIDsagn------------------------- 140 Bacillus haloduran...
2DEO_A     65 Qsk---iPVIIYVyppgaSAASAGTYIALGsh--lIAXAPGTSIGacrPILgysqng----------------------- 116 Pyrococcus horikoshii
ABX56715  125 Asrg-kkPVRAYVg---gDGCSAAYWITTAcd--rVTMDATARVGsigTVVsfvkrpdaegakrfefvss-------qsp 191 Vibrio shilonii
3BF0_A    366 AaraagkPVVVSMg---gMAASGGYWISTPan--yIVANPSTLTGsigIFGvittvensldsigvhtdgvst---splad 437 Escherichia coli
1Y7O_A    101 Fik---aDVQTIVx---gXAASXGTVIASSgakgkRFXLPNAEYXihqPXGgtgggtq---------------------- 152 Streptococcus pneu...
Feature 1                                                                                  
1TYF_A    133 ---------tdieihAREILKVKGRMNELMAlhtgqsle------------qierdterDRFLSAPEAVEYGLVDSI 188 Escherichia coli
3BEZ_A    438 vsitralppeaqlxxQLSIENGYKRFITLVAdarhstpe-------------qidkiaqGHVWTGQDAKANGLVDSL 501 Escherichia coli
3BEZ_A    189 pfirddxspaareadSRWIGELWQNYLNTVAanrqipaeqvfp-----gaqgllegltkTGGDTAKYALENKLVDAL 260 Escherichia coli
3BPP_A    117 ---------siieapPAITNYFIAYIKSLAQesgrnati-------------aeefitkDLSLTPEEALKYGVIEVV 171 Pyrococcus horikoshii
NP_242222 141 ------------aadEKAQSYWLAEMRNAAEyndrdpkyalamadrsieipeldisneeLLTLTASQALEVNYAEAI 205 Bacillus halodurans C...
2DEO_A    117 ---------siieapPKITNYFIAYIKSLAQesgrnati-------------aeefitkDLSLTPEEALKYGVIEVV 171 Pyrococcus horikoshii
ABX56715  192 nkrldpeseqgqtaiQTQLDAMAEVFISRVArnmgvtsd------------kvksdfgqGGVKIGQQAVDAGMAHEL 256 Vibrio shilonii
3BF0_A    438 vsitralppeaqlmmQLSIENGYKRFITLVAdarhstpe-------------qidkiaqGHVWTGQDAKANGLVDSL 501 Escherichia coli
1Y7O_A    153 --------qtdmaiaPEHLLKTRNTLEKILAensgqsxe------------kvhadaerDNWXSAQETLEYGFIDEI 209 Streptococcus pneumoniae

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