Conserved Protein Domain Family
Clp_protease_NfeD_like

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cd07021: Clp_protease_NfeD_like 
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease.
Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). 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 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.
Statistics
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PSSM-Id: 132932
View PSSM: cd07021
Aligned: 37 rows
Threshold Bit Score: 113.837
Threshold Setting Gi: 171184786
Created: 2-Dec-2008
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
active sitedimer interface
Feature 1:active site residues [active site]
Evidence:
  • Comment:The catalytic site consists of a Ser-Lys dyad and specifically cleaves C-terminal hydrophobic region of p-stomatin. In this example, catalytic Lys had been mutated to Ala.
  • Comment:structures of closely related sequences suggest that the binding of substrate to catalytic site induces conformational changes such that the catalytic Lys approaches the catalytic Ser.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                   #    
NP_242222     39 VYYIPVEQEverglEAFLQRSLDSAVEegadHIVLEINTPGGrvDAAGNMARALRETd---IPITAYVi--DQALSAGAY 113 Bacillus halodu...
YP_001056214  19 VVVVYLDGTvdgtaASLVSAALAEAEGrg-vPLLIVLDTYGGflQPTDQIVDAILRAr---VEVYAYVprgGKAMSAGAF 94  Pyrobaculum cal...
YP_023993     31 VLIINLTEEid-pgSSNMFHAMSKNYS----AVVIYMNTPGGilENMLQMVNCINKTeqrgIPVYTYVpddGMAASAGSY 105 Picrophilus tor...
YP_001793705  19 AVVVKLDGTidgtaVTLVERGLEAAEArg-lPLVLVIDTPGGflLPMEKIVKLVESAr---VPVYAYVpdaARAASAGAF 94  Thermoproteus n...
NP_560082     23 AVALYLDGVidgtaVTLASAALAEAQRlh-lPLVVIIDTYGGflAPMDQIVEMFLNAg---VPVYAYIpdgAKAMSAGAF 98  Pyrobaculum aer...
YP_001938749  50 VYVLPIRDEieqsmVYFVRRAVNEAMKngaqGLILDIDTPGGlaNSMEKIIRELERFpl-qENTYAFId--HKAYSAGAF 126 Methylokorus in...
YP_920234     27 VVVVDLEGRidegaYYTVKRGLEEADKg---VVVVVIRSYGGylKSMDKIVELLVSSe---ARTIAWVppgERTVSAAAV 100 Thermofilum pen...
YP_001527907  31 VYVVKVAGDvapgmAAYLKRALDDIPEaphqTIVLDLDTFGGrvDSALMIVDLITAAds-kGKTIAFVs--RKAISAGAL 107 Desulfococcus o...
YP_001818546  55 IYVIPVREQigsavLYVVRRGIKEAIEqraeAVIFDMDTPGGalDKTMSIMEAIGRFp---GRTLTYVn--TDAISAGAF 129 Opitutus terrae...
CAJ71842      92 TYVITIHRMidgglNSSIQRRVDSAKDknagLIIFDIDTFGGrlDAAMEISEFISDLk--eAKTVAFIs--HKAISAGAL 167 Candidatus Kuen...
Feature 1                                               #                                        
NP_242222    114 IALNADeIVMAPGSTMGSaaVIDSagn--------aadEKAQSYWLAEMRNAAEyNDRD--PKYALAMADRSi-----EI 178 Bacillus halodu...
YP_001056214  95 IAIAADrLYMDPTGEIGAaePRPPd-------------PKAVNYAEGRMRALAQrKWNDsrVDVAASFVRENrvltgrEA 161 Pyrobaculum cal...
YP_023993    106 VAMASDyIYMGSGSYIGPstPIVVggtp-------leeNHTKNAMAALMESMAIgHKRN--ETAAYSMVINNtaytsnEA 176 Picrophilus tor...
YP_001793705  95 IALAAErLYMAPTAVIGAaqPRPPd-------------PKVVNYAAAKMRALAArRWNDtrVQLAESFVTENkaltgaEA 161 Thermoproteus n...
NP_560082     99 IAMSARkIYMAPTAEIGAaePRPPd-------------PKVVNYAAARMRALAStKWNDtrLYIAESFVRENrvltgaEA 165 Pyrobaculum aer...
YP_001938749 127 IAACCRhIYMAPGSVIGAatPVVFspqggvqnlpesyeRKMLSAYQGLIRAIADrHGHN--PAVFNAMVDKDsg---lNI 201 Methylokorus in...
YP_920234    101 IALSAQrLYMGKGAVIGSikPYPDd-------------PKTVEYVVARVAALLSkKGVNdsRGLARRLVVDAqsftsdEA 167 Thermofilum pen...
YP_001527907 108 IALACNeLVMKPGTTIGDcaPIMVgsqgp-----emlgEKFQSPLRAKFRALAKkNGYP--EALAESMVTADm-----EV 175 Desulfococcus o...
YP_001818546 130 ISATTDeIWFAPRGKIGAaaPVGMsgqdi----dktmrQKVVSYLKAEVRSLSEgKGYR--GQVVSAMIDEDy-----EL 198 Opitutus terrae...
CAJ71842     168 IALSCNdIIMAPDAELGDcePILPttegg----yksagEKIQTVLRTKFRKFAEkNGYP--VLLAEAMVTSEi-----EV 236 Candidatus Kuen...
Feature 1                                                                                  
NP_242222    179 PELDIsn----------------------------eeLLTLTASQALEVNY---------AEAIasnrAELLEH 215 Bacillus halodurans C...
YP_001056214 162 VALGLaeppppggwei----------vaeykrdplmrLLNALSDPTLVALLlllgavligYELLaagfQGVGVV 225 Pyrobaculum calidifon...
YP_023993    177 YKIGLingicnnfteflkdm--vhgryiyvnenlydqFLSFLSNPEVSGLLiligffailIDLYhg-sIILSVI 247 Picrophilus torridus ...
YP_001793705 162 VAAGIaeppppiepa------------avverdpllrLLNALSDPALLVAMliagaalilYEVAtsgfQGLGVI 223 Thermoproteus neutrop...
NP_560082    166 ARLGMaeppppdgwnf----------vsvlrrdplsrLLNALSDPALISLMlllgvvligYELFasgfQGVGVI 229 Pyrobaculum aerophilu...
YP_001938749 202 DGVEIlpk---------------------------gkILTLTDSEACKKYGhppr--pllAEGIaqnlEELAQK 246 Methylokorus infernor...
YP_920234    168 VATGIadgtadslaellqkeglsfasvhyvsgdlvsdLLSVLLDPALAVLLallgamlllLEFKvtgfQGWGVI 241 Thermofilum pendens H...
YP_001527907 176 FRVVTkd----------------------------ggTFYMDALEYEEMDEa--------QKSAvvskKTVVAK 213 Desulfococcus oleovor...
YP_001818546 199 KIGDTvlkp-------------------------kgeLLTLTASEAAKTYGeppq--pllSAGTadtlEQLVTQ 245 Opitutus terrae PB90-1
CAJ71842     237 YRIETeen---------------------------peGFYISSRELKEMGE---------EDQKkikkKKLIVE 274 Candidatus Kuenenia s...

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