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
View PSSM: cd00394
Aligned: 9 rows
Threshold Bit Score: 133.672
Threshold Setting Gi: 163311059
Created: 6-Mar-2002
Updated: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
Feature 1                                                                                        
1TYF_A        28 VIFLTGqved-------------------------hmaNLIVAQMLFLEAenpekDIYLYINSpgg-vitAGMSIYDTMQ 81
3BEZ_A       305 VVFANGaixdgee------------------tqgnvggDTTAAQIRDARLdpkvkAIVLRVNSpgg-svtASEVIRAELA 365
3BEZ_A        35 LLDISGvivdkpdssqrfsklsrqllgassdrlqenslFDIVNTIRQAKDdrnitGIVXDLKNfaggdqpSXQYIGKALK 114
3BPP_A        12 VAQIKGqits-------------------------ytyDQFDRYITIAEQdn-aeAIIIELDTpgg-radAMMNIVQRIQ 64
gi 15613919   41 YIPVEQever-------------------------gleAFLQRSLDSAVEeg-adHIVLEINTpgg-rvdAAGNMARALR 93
2DEO_A        12 VAQIKGqits-------------------------ytyDQFDRYITIAEQdn-aeAIIIELDTpgg-radAXXNIVQRIQ 64
gi 161087235  60 IIHVNGvisryanlf--------------havcggvstEVLAKEFNAALNessvkAVILNVDSpgg-easGIHELSEMIH 124
3BF0_A       305 VVFANGaimdgee------------------tqgnvggDTTAAQIRDARLdpkvkAIVLRVNSpgg-svtASEVIRAELA 365
1Y7O_A        47 IIXLTGpved-------------------------nxaNSVIAQLLFLDAqdstkDIYLYVNTpgg-svsAGLAIVDTXN 100
                         90       100       110       120       130       140       150       160
Feature 1                             #                                                          
1TYF_A        82 Fik---pDVSTICm---gQAASMGAFLLTAgakgkRFCLPNSRVMihqPLGgyqgqa----------------------- 132
3BEZ_A       366 AaraagkPVVVSXg---gXAASGGYWISTPan--yIVANPSTLTGsigIFGvittvensldsigvhtdgvst---splad 437
3BEZ_A       115 EfrdsgkPVYAVGe----NYSQGQYYLASFan--kIWLSPQGVVDlhgFATnglyykslldklkvsthvfrvgtyksave 188
3BPP_A        65 Qsk---iPVIIYVyppgaSAASAGTYIALGsh--lIAMAPGTSIGacrPILgysqng----------------------- 116
gi 15613919   94 Etd---iPITAYVi---dQALSAGAYIALNad--eIVMAPGSTMGsaaVIDsagn------------------------- 140
2DEO_A        65 Qsk---iPVIIYVyppgaSAASAGTYIALGsh--lIAXAPGTSIGacrPILgysqng----------------------- 116
gi 161087235 125 Asrg-kkPVRAYVg---gDGCSAAYWITTAcd--rVTMDATARVGsigTVVsfvkrpdaegakrfefvss-------qsp 191
3BF0_A       366 AaraagkPVVVSMg---gMAASGGYWISTPan--yIVANPSTLTGsigIFGvittvensldsigvhtdgvst---splad 437
1Y7O_A       101 Fik---aDVQTIVx---gXAASXGTVIASSgakgkRFXLPNAEYXihqPXGgtgggtq---------------------- 152
                        170       180       190       200       210       220       230
Feature 1                                                                                     
1TYF_A       133 ---------tdieihAREILKVKGRMNELMAlhtgqsle------------qierdterDRFLSAPEAVEYGLVDSI 188
3BEZ_A       438 vsitralppeaqlxxQLSIENGYKRFITLVAdarhstpe-------------qidkiaqGHVWTGQDAKANGLVDSL 501
3BEZ_A       189 pfirddxspaareadSRWIGELWQNYLNTVAanrqipaeqvfp-----gaqgllegltkTGGDTAKYALENKLVDAL 260
3BPP_A       117 ---------siieapPAITNYFIAYIKSLAQesgrnati-------------aeefitkDLSLTPEEALKYGVIEVV 171
gi 15613919  141 ------------aadEKAQSYWLAEMRNAAEyndrdpkyalamadrsieipeldisneeLLTLTASQALEVNYAEAI 205
2DEO_A       117 ---------siieapPKITNYFIAYIKSLAQesgrnati-------------aeefitkDLSLTPEEALKYGVIEVV 171
gi 161087235 192 nkrldpeseqgqtaiQTQLDAMAEVFISRVArnmgvtsd------------kvksdfgqGGVKIGQQAVDAGMAHEL 256
3BF0_A       438 vsitralppeaqlmmQLSIENGYKRFITLVAdarhstpe-------------qidkiaqGHVWTGQDAKANGLVDSL 501
1Y7O_A       153 --------qtdmaiaPEHLLKTRNTLEKILAensgqsxe------------kvhadaerDNWXSAQETLEYGFIDEI 209

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