2DEO,3BPP


Conserved Protein Domain Family
Clp_protease_NfeD_1

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cd07020: Clp_protease_NfeD_1 
Click on image for an interactive view with Cn3D
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: 132931
View PSSM: cd07020
Aligned: 51 rows
Threshold Bit Score: 193.54
Threshold Setting Gi: 145591605
Created: 2-Dec-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active sitedimer interface
Conserved site includes 2 residues -Click on image for an interactive view with Cn3D
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:Structure suggests that the binding of substrate to catalytic site induces conformational changes such that the catalytic Lys approaches the catalytic Ser.
  • Comment:The 1510-N protease specifically cleaves the C-terminal hydrophobic region of p-stomatin, PH1511
  • Structure:3BPP: Pyrococcus horikoshii 1510-N membrane protease K138A mutant
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                 #      
2DEO_A        10 VYVAQIKGqitsyTYDQFDRYITIAEQdnaeAIIIELDTPGGraDAXXNIVQRIQQSkIPVIIYVyppgASAASAGTYIA 89  Pyrococcus hori...
3BPP_A        10 VYVAQIKGqitsyTYDQFDRYITIAEQdnaeAIIIELDTPGGraDAMMNIVQRIQQSkIPVIIYVyppgASAASAGTYIA 89  Pyrococcus hori...
YP_001917904  43 YKLLTVEDtitagTSQYLEQGIENAINqgydGVIIVLNTPGGlvDATLDIMGKIVNSpIPVITFVspsgAIAASAGTFIL 122 Natranaerobius ...
NP_615868     35 VLVLEISGaitpaSDNLIADAIQSAESgnyeALVITLDTPGGglEETQIIIKAIENTtMPVIGYVpe-sGKAWSAGTLIL 113 Methanosarcina ...
YP_844137     22 VVSLRIDGaitpaSDDLVKTAIGYAESsnadALILMLDTPGGglSETLEIIAVVERTeIPVVGYVspsgAKAWSAGTMIL 101 Methanosaeta th...
NP_070609     32 VAKVEVRGeinqgTYLTLQHAYDFALRerfdVLFVVLDTPGGllSSTQKIVKMFLNSeVPVVVFVpr-gAMCASAGSIIL 110 Archaeoglobus f...
YP_001040178  29 IVTVNINGeinygTQYLLEEALSEAEKld-aPLIMILDTPGGllDSANNMIKLIRNSnVPVIGYVypagAQAWSAGTLIL 107 Staphylothermus...
YP_566439     31 VLVLDISDsitpvADDLVIDALQLAEQneyeALIITLNTPGGgvDETLKIIEAIDRSdIPVIGYVypggTKAWSAGTLIL 110 Methanococcoide...
YP_001736768  25 VLVTNITGyispaTVEQVKLAVKTAENgy-sALVLQINTFGGqsDATFSIIDLILASkVPVIGYVypegGQALSAGTYIL 103 Candidatus Kora...
YP_359707     26 VLATRVEGvidpvIAGHLKEIIQKAEReeasFVLIELNTPGGldTSMREITSAILAAkVPVGVWVgpsgARAASAGTFIL 105 Carboxydothermu...
Feature 1                                           #                                            
2DEO_A        90 LGSHlIAXAPGTSIGACRPILgysqng-siieapPKITNYFIAYIKSLAQeSGRNATIAEEFITkDLSLTPEEALKYGVI 168 Pyrococcus hori...
3BPP_A        90 LGSHlIAMAPGTSIGACRPILgysqng-siieapPAITNYFIAYIKSLAQeSGRNATIAEEFITkDLSLTPEEALKYGVI 168 Pyrococcus hori...
YP_001917904 123 VSGHvAAMTPGSTCGAAMPVTmqpgee-gtqeadQKTINFLAGHLKSVAReQGRPEEVVEKFVTeNLTLNASEALEKNVI 201 Natranaerobius ...
NP_615868    114 MGTDiAAMAPFTVIGSAQPVQvsaegt--vpvedEKTINALVKFSTETARkHGRNETFAEEVITeNRNLNAEEALEEGVI 191 Methanosarcina ...
YP_844137    102 ISTDiAAMAPNTIIGSAQPVRllptga-tepvndTKTTNAIVALIEEKAKiHGRNRTAAREFVLsNLNLNAEEALEYGVI 180 Methanosaeta th...
NP_070609    111 LSSHiAVMADGTAVGAATPVSvgfas----aeveNKTVNYIAGYVKDIAReRGRNEGVAEKFVTqALTLTAKEALEQGII 186 Archaeoglobus f...
YP_001040178 108 LATHiAAMAPGTLIGAAQPVLydpttgtfkpineSKIINPIVGIITTLAEdRGRNKTAAELFVRkNLYLTAEKALKYHVI 187 Staphylothermus...
YP_566439    111 IGTDiAAMSPNTIIGSAQPVSvspqgi--epiedDKIVNALVALAKTKAKqHGRNETTAEKFITeNLNLNDEEALEAGII 188 Methanococcoide...
YP_001736768 104 MATDyAAMSPYSTIGSAQPVVgytp------lneSKYLNAYATKMRSYAAmHGRNQSAAELMVLsNKNFMADEALKVGLI 177 Candidatus Kora...
YP_359707    106 YSAQvAAMAPQTTIGSAHPVNlggqsl--dqdlrAKVENDAVSYITSLAKrNGRNPVWAEEAVRkSVSVDAEEAYKKGII 183 Carboxydothermu...
Feature 1                                      
2DEO_A       169 EVVArdiNELLKKsnGXKTKIpvngrYVTL 198 Pyrococcus horikoshii
3BPP_A       169 EVVArdiNELLKKsnGMKTKIpvngrYVTL 198 Pyrococcus horikoshii
YP_001917904 202 EFNEpnlDALLTAihGHEVTVag--eEITL 229 Natranaerobius thermophilus JW/NM-WN-LF
NP_615868    192 EYIAisvPNLLNQvdGEIVKGk---eLHTA 218 Methanosarcina acetivorans C2A
YP_844137    181 EHVSpdiSSLLKSinGSSAKNr---tLVTE 207 Methanosaeta thermophila PT
NP_070609    187 DYIAnteGEAIEGlkGRSAEIdg--kLVTF 214 Archaeoglobus fulgidus DSM 4304
YP_001040178 188 EVIAlnmDDLINKidGWTVKLdngreYVLR 217 Staphylothermus marinus F1
YP_566439    189 EYVAsdiDDLLEQvnGQMIKGk----VLNT 214 Methanococcoides burtonii DSM 6242
YP_001736768 178 DSVEqslDSLLENadGKVVRRga--qEFKL 205 Candidatus Korarchaeum cryptofilum OPF8
YP_359707    184 NFIAknpEEFLEKahGLRVKVsg--sELVL 211 Carboxydothermus hydrogenoformans Z-2901

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