3BPP,2DEO


Conserved Protein Domain Family
Clp_protease_NfeD

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cd07015: Clp_protease_NfeD 
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: 132926
View PSSM: cd07015
Aligned: 3 rows
Threshold Bit Score: 258.477
Threshold Setting Gi: 15613919
Created: 26-Nov-2008
Updated: 17-Jan-2013
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.
  • 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                                                                              #      
3BPP_A     10 VYVAQIKGqitsytYDQFDRYITIAEQdnaeAIIIELDTPGgraDAMMNIVQRIQQSkIPVIIYVyppgASAASAGTYIA 89  Pyrococcus horikoshii
2DEO_A     10 VYVAQIKGqitsytYDQFDRYITIAEQdnaeAIIIELDTPGgraDAXXNIVQRIQQSkIPVIIYVyppgASAASAGTYIA 89  Pyrococcus horikoshii
NP_242222  39 VYYIPVEQeverglEAFLQRSLDSAVEegadHIVLEINTPGgrvDAAGNMARALRETdIPITAYVi---DQALSAGAYIA 115 Bacillus haloduran...
Feature 1                                       #                                             
3BPP_A     90 LGSHlIAMAPGTSIGAcrPILgysqngsiieapPAITNYFIAYIKSLAQesg-----------rnaTIAEEFIt--kDLS 156 Pyrococcus horikoshii
2DEO_A     90 LGSHlIAXAPGTSIGAcrPILgysqngsiieapPKITNYFIAYIKSLAQesg-----------rnaTIAEEFIt--kDLS 156 Pyrococcus horikoshii
NP_242222 116 LNADeIVMAPGSTMGSaaVIDsagn-----aadEKAQSYWLAEMRNAAEyndrdpkyalamadrsiEIPELDIsneeLLT 190 Bacillus haloduran...
Feature 1                              
3BPP_A    157 LTPEEALKYGVIEVVardiNELLKK 181 Pyrococcus horikoshii
2DEO_A    157 LTPEEALKYGVIEVVardiNELLKK 181 Pyrococcus horikoshii
NP_242222 191 LTASQALEVNYAEAIasnrAELLEH 215 Bacillus halodurans C-125

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