Conserved Protein Domain Family
pepsin_A_like_plant

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cd05476: pepsin_A_like_plant 
Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants.
This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH.
Statistics
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PSSM-Id: 133143
View PSSM: cd05476
Aligned: 79 rows
Threshold Bit Score: 153.573
Threshold Setting Gi: 115465777
Created: 14-Jan-2008
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
catalytic motifcatalyticActive site
Feature 1:catalytic motif [active site]
Evidence:
  • Comment:Catalytic motif in both N- and C-terminal lobes of this family.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                           ####                                                         
NP_171637    141 EYFTRLGVGTParYVYMVLDTGSDIVWLQCapcrrcysqsdpifdprksktya--------tipcssphcrrldsagcnt 212 thale cress
EDQ61569      36 LYYTKIYLGTPpvGYYVQVDTGSDVTWLNCapctscvtetqlpsiklttydpsrsstdgalscrdsncgaalgsnevsct 115 Physcomitrella ...
NP_563808     83 LYYTKVKLGTPprEFNVQIDTGSDVLWVSCtscngcpktselqiqlsffdpgvsss--aslvscsdrrcysnfqtesgcs 160 thale cress
Q9S9K4        73 LYFTKIKLGSPpkEYHVQVDTGSDILWINCkpcpkcptktnlnfrlslfdmnasst---skkvgcdddfcsfisqsdscq 149 thale cress
XP_001690254  12 YFYTTLKLGTPerTFSVIIDTGSTITYIPCkdcshcgkhtaewfdpdksttak---------klacgdplcncgtpsctc 82  Chlamydomonas r...
AAV59271      92 YYTTRLWIGTPpqMFALIVDSGSTVTYVPCsdceqcgkhqdpkfqpemss---------------tyqpvkcnmdcncdd 156 thale cress
EDQ75547      98 YYTSRVFIGTPaqEFALIVDTGSTVTYVPCsscthcghhqacfdprfkpdnss--------syqtvscnspdcitkmcda 169 Physcomitrella ...
XP_001422234  38 TLVAEYALADGq-TYDLIVDTGSARTYVPCkgcarcgehahgyydydrsmeferl-----dcgeasdatlceetmkgtcq 111 Ostreococcus lu...
CAL58575      34 VLVASFELAGAq-TFELIVDTGSSRTYLPCkgcascgaheagryydydasad-----------fsrvecsacagiggkcg 101 Ostreococcus tauri
EAZ40507      90 YYTTRLYIGTPsqEFALIVDSGSTVTYVPCatceqcgnhqsespniieahdprfq-----pdlsstyspvkcnvdctcdn 164 Japanese rice
Feature 1                                                                                        
NP_171637    213 rrktCLYQVSYGdGSFTVGDFsTETLTFrrn--------rvkGVALGCghdne----glfvgAAGLLGLGKGKLSFPGQT 280 thale cress
EDQ61569     116 sagyCAYSTTYGdGSSTQGYFiQDVMTFqeihnnt-qvngtaSVYFGCgttqsgnllmssraLDGLIGFGQAAVSIPSQL 194 Physcomitrella ...
NP_563808    161 pnnlCSYSFKYGdGSGTSGYYiSDFMSFdtvitstlainssaPFVFGCsnlqsgdlqrprraVDGIFGLGQGSLSVISQL 240 thale cress
Q9S9K4       150 palgCSYHIVYAdESTSDGKFiRDMLTLeqvtgdlktgplgqEVVFGCgsdqsgqlgngdsaVDGVMGFGQSNTSVLSQL 229 thale cress
XP_001690254  83 nndrCYYSRTYAeRSSSEGWMiEDTFGFpdsd-------spvRLVFGCengetg--eiyrqmADGIMGMGNNHNAFQSQL 153 Chlamydomonas r...
AAV59271     157 dreqCVYEREYAeHSSSKGVLgEDLISFgnesq-----ltpqRAVFGCetvetg--dlysqrADGIIGLGQGDLSLVDQL 229 thale cress
EDQ75547     170 rvhqCKYERVYAeMSSSKGVLgKDLLGFgngsr-----lqphPLLFGCetaetg--dlylqhADGIMGLGRGPLSIVDQL 242 Physcomitrella ...
XP_001422234 112 sdgrCSYVVSYAeGSSSRGYVvRDRVRLgegt-------lsaMLAFGCeeaetn--aiyeqkADGLFGFGRGTATVHAQL 182 Ostreococcus lu...
CAL58575     102 tsgvCRYDVHYLeGSGSEGYLvRDVVSLggsv-------gnaTVVFGCeerelg--sikqqsADGLFGFGRQAYALRAQL 172 Ostreococcus tauri
EAZ40507     165 ersqCTYERQYAeMSSSSGVLgEDIMSFgkese-----lkpqRAVFGCentetg--dlfsqhADGIMGLGRGQLSIMDQL 237 Japanese rice
Feature 1                                                                                        
NP_171637    281 GHrf--nqKFSYCLvdrs---asskPSSVVFGNAav---srIARFTPLlsnpkldtFYYVGLlgisvggtrvpgvtaslf 352 thale cress
EDQ61569     195 ASmgkvgnRFAHCLqgd-----nqgGGTIVIGSVse----pNISYTPIvs----rnHYAVGMqniavngrnvtt--pasf 259 Physcomitrella ...
NP_563808    241 AVqglaprVFSHCLkgd-----ksgGGIMVLGQIkr----pDTVYTPLvps---qpHYNVNLqsiavngqilpi---dps 305 thale cress
Q9S9K4       230 AAtgdakrVFSHCLdnv------kgGGIFAVGVVds----pKVKTTPMvpn---qmHYNVMLmgmdvdgtsl------dl 290 thale cress
XP_001690254 154 VQrkviedVFSLCFgy-------pkDGILLLGDVtlp-egaNTVYTPLlthl-hlhYYNVKMdgitvngqtla-----fd 219 Chlamydomonas r...
AAV59271     230 VDkglisnSFGLCYggm-----dvgGGSMILGGFdy---psDMVFTDSdpd--rspYYNIDLtgirvagkqls-----lh 294 thale cress
EDQ75547     243 VGtgamedSFSLCYggm-----degGGSMVLGAIpp---ppAMVFAKSdpn--rsnYYNLELseiqvqgvsln-----vp 307 Physcomitrella ...
XP_001422234 183 ASaglienVFSFCVegf-----ganGGVLTLGRFdfgadapALARTPLvadpanpaFHNVRTsswklgds---------- 247 Ostreococcus lu...
CAL58575     173 ASasviddLFSMCVegyeklsgehvGGLLTLGNFdfgadapALVYTPMvss---amYYQVTTtswtlgns---------- 239 Ostreococcus tauri
EAZ40507     238 VEkgvisdSFSLCYggm-----dvgGGTMVLGGMpa---ppDMVFSHSnpv--rspYYNIELkeihvagkalr-----ld 302 Japanese rice
Feature 1                    ####                                                                
NP_171637    353 kldqigngGVIIDSGTSVTRLIRPAYiamrdafrvgaktlkrapd---------------------------------fs 399 thale cress
EDQ61569     260 dttstsagGVIMDSGTTLAYLVDPAYtqfvnavstfessmfss------------------------------------- 302 Physcomitrella ...
NP_563808    306 vftiatgdGTIIDTGTTLAYLPDEAYspfiqavanavsqygrpi----------------------------------ty 351 thale cress
Q9S9K4       291 prsivrngGTIVDSGTTLAYFPKVLYdslietilarqpvklhiv-----------------------------------e 335 thale cress
XP_001690254 220 asvfdrgyGTVLDSGTTFTYLPTDAFkamakavgdyvekkglqstpgad-------------------------pqyndi 274 Chlamydomonas r...
AAV59271     295 srvfdgehGAVLDSGTTYAYLPDAAFaafeeavmrevstlkqidgpdp--------------------------nfkdtc 348 thale cress
EDQ75547     308 sevfngrlGTVLDSGTTYAYLPDKAFdafkdaitqqlgslqavpgpdp---------------------------sypdv 360 Physcomitrella ...
XP_001422234 248 liehlnsyTTTLDSGTTFTFVPRSVWvsfktrldtqatqagleivagpdpqy-------------------ddvcygvsa 308 Ostreococcus lu...
CAL58575     240 vvegsrgvLTIIDSGTSYTYVPGNMHarflqlaedaaresglekvappe-------------------------dypdlc 294 Ostreococcus tauri
EAZ40507     303 pkifnskhGTVLDSGTTYAYLPEQAFvafkdailfilflfssslsflkmeifkmdtpgkvtnkvnslkkirgpdpnykdi 382 Japanese rice
Feature 1                                                                                        
NP_171637    400 lfdtcfdlsnmnevkvPTVVLHFr---------gADVSLpatnylipvdtngkFCFAFagt------mggLSIIGNIQQQ 464 thale cress
EDQ61569     303 hsqclqlawcslqadfPTVKLFFdagavmnltprNYLYSqplqn-----gqaaYCMGWqksttk-agylsYSILGDIVLK 376 Physcomitrella ...
NP_563808    352 esyqcfeitagdvdvfPQVSLSFaggasmvlgprAYLQIfsss------gssiWCIGFqrms-----hrrITILGDLVLK 420 thale cress
Q9S9K4       336 etfqcfsfstnvdeafPPVSFEFedsvkltvyphDYLFTlee---------elYCFGWqagglttderseVILLGDLVLS 406 thale cress
XP_001690254 275 cwkgapdqfkdldkyfPPAEFVFgggakltlpplRYLFLskp---------aeYCLGIfdn------gnsGALVGGVSVR 339 Chlamydomonas r...
AAV59271     349 fqvaasnyvselskifPSVEMVFksgqswllspeNYMFRhskv-------hgaYCLGVfpng-----kdhTTLLGGIVVR 416 thale cress
EDQ75547     361 cfagagsdskalgkhfPPVDFVFsgnqkvflapeNYLFKhtkv-------pgaYCLGFfkn------qdaTTLLGGIVVR 427 Physcomitrella ...
XP_001422234 309 aamnmtlsqstvsewfPPLTIAYeggvsltlgpeNYLFAhetn-------saaFCVGIfan------pnnQILLGQITMR 375 Ostreococcus lu...
CAL58575     295 fgnsgglgwstvseyfPALKIEYhgsarltlspeTYLYWhqkn-------asaFCVGIleh------ddnRILLGQITMR 361 Ostreococcus tauri
EAZ40507     383 cfagagrnvsqlsevfPDVDMVFgngqklslspeNYLFRhskv-------egaYCLGVfqng-----kdpTTLLGGIVVR 450 Japanese rice
Feature 1                            
NP_171637    465 GFRVVYDLassRVGFAPGGC 484 thale cress
EDQ61569     377 DHLVVYDNdnrVVGWKSFDC 396 Physcomitrella patens subsp. patens
NP_563808    421 DKVVVYDLvrqRIGWAEYDC 440 thale cress
Q9S9K4       407 NKLVVYDLdneVIGWADHNC 426 thale cress
XP_001690254 340 DVVVTYDRrnsKVGFTTMAC 359 Chlamydomonas reinhardtii
AAV59271     417 NTLVVYDRensKVGFWRTNC 436 thale cress
EDQ75547     428 NTLVTYDRanhQIGFFKTNC 447 Physcomitrella patens subsp. patens
XP_001422234 376 DTLMEFDVansRVGMAPANC 395 Ostreococcus lucimarinus CCE9901
CAL58575     362 NTFTEFDVarsQVGMASANC 381 Ostreococcus tauri
EAZ40507     451 NTLVTYDRhneKIGFWKTNC 470 Japanese rice

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