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: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                           ####                                                         
gi 15223368  141 EYFTRLGVGTParYVYMVLDTGSDIVWLQCapcrrcysqsdpifdprksktya--------tipcssphcrrldsagcnt 212
gi 162675069  36 LYYTKIYLGTPpvGYYVQVDTGSDVTWLNCapctscvtetqlpsiklttydpsrsstdgalscrdsncgaalgsnevsct 115
gi 18390865   83 LYYTKVKLGTPprEFNVQIDTGSDVLWVSCtscngcpktselqiqlsffdpgvsss--aslvscsdrrcysnfqtesgcs 160
gi 118572746  73 LYFTKIKLGSPpkEYHVQVDTGSDILWINCkpcpkcptktnlnfrlslfdmnasst---skkvgcdddfcsfisqsdscq 149
gi 159464048  12 YFYTTLKLGTPerTFSVIIDTGSTITYIPCkdcshcgkhtaewfdpdksttak---------klacgdplcncgtpsctc 82
gi 55733749   92 YYTTRLWIGTPpqMFALIVDSGSTVTYVPCsdceqcgkhqdpkfqpemss---------------tyqpvkcnmdcncdd 156
gi 162689174  98 YYTSRVFIGTPaqEFALIVDTGSTVTYVPCsscthcghhqacfdprfkpdnss--------syqtvscnspdcitkmcda 169
gi 145356007  38 TLVAEYALADGq-TYDLIVDTGSARTYVPCkgcarcgehahgyydydrsmeferl-----dcgeasdatlceetmkgtcq 111
gi 116056042  34 VLVASFELAGAq-TFELIVDTGSSRTYLPCkgcascgaheagryydydasad-----------fsrvecsacagiggkcg 101
gi 125600931  90 YYTTRLYIGTPsqEFALIVDSGSTVTYVPCatceqcgnhqsespniieahdprfq-----pdlsstyspvkcnvdctcdn 164
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 15223368  213 rrktCLYQVSYGdGSFTVGDFsTETLTFrrn--------rvkGVALGCghdne----glfvgAAGLLGLGKGKLSFPGQT 280
gi 162675069 116 sagyCAYSTTYGdGSSTQGYFiQDVMTFqeihnnt-qvngtaSVYFGCgttqsgnllmssraLDGLIGFGQAAVSIPSQL 194
gi 18390865  161 pnnlCSYSFKYGdGSGTSGYYiSDFMSFdtvitstlainssaPFVFGCsnlqsgdlqrprraVDGIFGLGQGSLSVISQL 240
gi 118572746 150 palgCSYHIVYAdESTSDGKFiRDMLTLeqvtgdlktgplgqEVVFGCgsdqsgqlgngdsaVDGVMGFGQSNTSVLSQL 229
gi 159464048  83 nndrCYYSRTYAeRSSSEGWMiEDTFGFpdsd-------spvRLVFGCengetg--eiyrqmADGIMGMGNNHNAFQSQL 153
gi 55733749  157 dreqCVYEREYAeHSSSKGVLgEDLISFgnesq-----ltpqRAVFGCetvetg--dlysqrADGIIGLGQGDLSLVDQL 229
gi 162689174 170 rvhqCKYERVYAeMSSSKGVLgKDLLGFgngsr-----lqphPLLFGCetaetg--dlylqhADGIMGLGRGPLSIVDQL 242
gi 145356007 112 sdgrCSYVVSYAeGSSSRGYVvRDRVRLgegt-------lsaMLAFGCeeaetn--aiyeqkADGLFGFGRGTATVHAQL 182
gi 116056042 102 tsgvCRYDVHYLeGSGSEGYLvRDVVSLggsv-------gnaTVVFGCeerelg--sikqqsADGLFGFGRQAYALRAQL 172
gi 125600931 165 ersqCTYERQYAeMSSSSGVLgEDIMSFgkese-----lkpqRAVFGCentetg--dlfsqhADGIMGLGRGQLSIMDQL 237
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 15223368  281 GHrf--nqKFSYCLvdrs---asskPSSVVFGNAav---srIARFTPLlsnpkldtFYYVGLlgisvggtrvpgvtaslf 352
gi 162675069 195 ASmgkvgnRFAHCLqgd-----nqgGGTIVIGSVse----pNISYTPIvs----rnHYAVGMqniavngrnvtt--pasf 259
gi 18390865  241 AVqglaprVFSHCLkgd-----ksgGGIMVLGQIkr----pDTVYTPLvps---qpHYNVNLqsiavngqilpi---dps 305
gi 118572746 230 AAtgdakrVFSHCLdnv------kgGGIFAVGVVds----pKVKTTPMvpn---qmHYNVMLmgmdvdgtsl------dl 290
gi 159464048 154 VQrkviedVFSLCFgy-------pkDGILLLGDVtlp-egaNTVYTPLlthl-hlhYYNVKMdgitvngqtla-----fd 219
gi 55733749  230 VDkglisnSFGLCYggm-----dvgGGSMILGGFdy---psDMVFTDSdpd--rspYYNIDLtgirvagkqls-----lh 294
gi 162689174 243 VGtgamedSFSLCYggm-----degGGSMVLGAIpp---ppAMVFAKSdpn--rsnYYNLELseiqvqgvsln-----vp 307
gi 145356007 183 ASaglienVFSFCVegf-----ganGGVLTLGRFdfgadapALARTPLvadpanpaFHNVRTsswklgds---------- 247
gi 116056042 173 ASasviddLFSMCVegyeklsgehvGGLLTLGNFdfgadapALVYTPMvss---amYYQVTTtswtlgns---------- 239
gi 125600931 238 VEkgvisdSFSLCYggm-----dvgGGTMVLGGMpa---ppDMVFSHSnpv--rspYYNIELkeihvagkalr-----ld 302
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                    ####                                                                
gi 15223368  353 kldqigngGVIIDSGTSVTRLIRPAYiamrdafrvgaktlkrapd---------------------------------fs 399
gi 162675069 260 dttstsagGVIMDSGTTLAYLVDPAYtqfvnavstfessmfss------------------------------------- 302
gi 18390865  306 vftiatgdGTIIDTGTTLAYLPDEAYspfiqavanavsqygrpi----------------------------------ty 351
gi 118572746 291 prsivrngGTIVDSGTTLAYFPKVLYdslietilarqpvklhiv-----------------------------------e 335
gi 159464048 220 asvfdrgyGTVLDSGTTFTYLPTDAFkamakavgdyvekkglqstpgad-------------------------pqyndi 274
gi 55733749  295 srvfdgehGAVLDSGTTYAYLPDAAFaafeeavmrevstlkqidgpdp--------------------------nfkdtc 348
gi 162689174 308 sevfngrlGTVLDSGTTYAYLPDKAFdafkdaitqqlgslqavpgpdp---------------------------sypdv 360
gi 145356007 248 liehlnsyTTTLDSGTTFTFVPRSVWvsfktrldtqatqagleivagpdpqy-------------------ddvcygvsa 308
gi 116056042 240 vvegsrgvLTIIDSGTSYTYVPGNMHarflqlaedaaresglekvappe-------------------------dypdlc 294
gi 125600931 303 pkifnskhGTVLDSGTTYAYLPEQAFvafkdailfilflfssslsflkmeifkmdtpgkvtnkvnslkkirgpdpnykdi 382
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 15223368  400 lfdtcfdlsnmnevkvPTVVLHFr---------gADVSLpatnylipvdtngkFCFAFagt------mggLSIIGNIQQQ 464
gi 162675069 303 hsqclqlawcslqadfPTVKLFFdagavmnltprNYLYSqplqn-----gqaaYCMGWqksttk-agylsYSILGDIVLK 376
gi 18390865  352 esyqcfeitagdvdvfPQVSLSFaggasmvlgprAYLQIfsss------gssiWCIGFqrms-----hrrITILGDLVLK 420
gi 118572746 336 etfqcfsfstnvdeafPPVSFEFedsvkltvyphDYLFTlee---------elYCFGWqagglttderseVILLGDLVLS 406
gi 159464048 275 cwkgapdqfkdldkyfPPAEFVFgggakltlpplRYLFLskp---------aeYCLGIfdn------gnsGALVGGVSVR 339
gi 55733749  349 fqvaasnyvselskifPSVEMVFksgqswllspeNYMFRhskv-------hgaYCLGVfpng-----kdhTTLLGGIVVR 416
gi 162689174 361 cfagagsdskalgkhfPPVDFVFsgnqkvflapeNYLFKhtkv-------pgaYCLGFfkn------qdaTTLLGGIVVR 427
gi 145356007 309 aamnmtlsqstvsewfPPLTIAYeggvsltlgpeNYLFAhetn-------saaFCVGIfan------pnnQILLGQITMR 375
gi 116056042 295 fgnsgglgwstvseyfPALKIEYhgsarltlspeTYLYWhqkn-------asaFCVGIleh------ddnRILLGQITMR 361
gi 125600931 383 cfagagrnvsqlsevfPDVDMVFgngqklslspeNYLFRhskv-------egaYCLGVfqng-----kdpTTLLGGIVVR 450
                        410       420
                 ....*....|....*....|
Feature 1                            
gi 15223368  465 GFRVVYDLassRVGFAPGGC 484
gi 162675069 377 DHLVVYDNdnrVVGWKSFDC 396
gi 18390865  421 DKVVVYDLvrqRIGWAEYDC 440
gi 118572746 407 NKLVVYDLdneVIGWADHNC 426
gi 159464048 340 DVVVTYDRrnsKVGFTTMAC 359
gi 55733749  417 NTLVVYDRensKVGFWRTNC 436
gi 162689174 428 NTLVTYDRanhQIGFFKTNC 447
gi 145356007 376 DTLMEFDVansRVGMAPANC 395
gi 116056042 362 NTFTEFDVarsQVGMASANC 381
gi 125600931 451 NTLVTYDRhneKIGFWKTNC 470

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