1YM4,1B11,1PPL,1G0V,1HTR,1TZS,3PEP,1QDM,1HRN,1T6G,1ZAP


Conserved Protein Domain Family
pepsin_retropepsin_like

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cd05470: pepsin_retropepsin_like 
Click on image for an interactive view with Cn3D
Cellular and retroviral pepsin-like aspartate proteases.
This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family).
Statistics
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PSSM-Id: 133137
View PSSM: cd05470
Aligned: 17 rows
Threshold Bit Score: 58.9307
Threshold Setting Gi: 6729982
Created: 7-Sep-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:inhibitor binding site
Evidence:
  • Structure:1b11_a,Feline Immunodeficiency Virus Protease complexed with inhibitor Tl-3-093.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       # # #                                                     ###   
1YM4_A       32 VEMTVgsppqtLNILVDTGSSNFAVGaaphpflhryyqr----------------------qlsstyrdlrkgvYVPYtq 89
1B11_A       13 ILIFVng--ypIKFLLDTGADITILNrrdfqvkn---------------------------------siengrqNMIGvg 57
1PPL_E       19 TPVTIgg--ttLNLNFDTGSADLWVFstelpasqqsghsvy-------------------npsatgkelsgytwSISYgd 77
1G0V_A       17 TDITLgtppqnFKVILDTGSSNLWVPsnecgslacflhsky------------------dheasssykangtefAIQYgt 78
1HRN_A       19 GEIGIgtppqtFKVVFDTGSSNVWVPsskcsrlytacvyhkl----------------fdasdsssykhngtelTLRYst 82
gi 62195942 127 VNGRVng--arVHFLVDTGASSVVLSqedaeragid-----------------------------taslnysvpIMTAng 175
gi 56118817  72 GVISIgtppqsFRVVFDTGSSNLWVPskkckwtdiacwlhrk----------------ydskksstykangtefAIHYgt 135
1T6G_B       18 IPFHDg-----ASLVLDVAGPLVWSTcdggqppaeipcssptcllana----ypapgcpapscgsdkhdkpctaYPYNpv 88
1ZAP_A       16 ADITVgsnnqkLNVIVDTGSSDLWVPdvnidcqvtysdqtadfckq---------kgtydpsgssasqdlntpfSIGYgd 86
gi 85001307  84 IYMGIgnpkvkQMLIIDTGSQQINVAcgnspscgkhsldnynyqnsvtykpidcesdsckiieggcdlerscifSETYse 163
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
Feature 1                                                            #   
1YM4_A       90 --gKWEGElg-tDLVSIphgpn------vtvrANIAAitesdkffingsnweGILGL 137
1B11_A       58 --gGKRGTnyinVHLEIrdenyk----tqcifGNVCVledn-------sliqPLLGR 101
1PPL_E       78 -gsSASGNvf-tDSVTVggvt--------ahgQAVQAaqqisaqfqqdtnndGLLGL 124
1G0V_A       79 --gSLEGYis-qDTLSIgdlt--------ipkQDFAEatsepgltfafgkfdGILGL 124
1HRN_A       83 --gTVSGFls-qDIITVggi---------tvtQMFGEvtempalpfmlaefdGVVGM 127
gi 62195942 176 --qARAASit-iATLQIgdie--------rhnVRAMVtkeg-------lltgSLLGM 214
gi 56118817 136 --gSLTGFls-tDTVSVgsls--------vksQTFAEaitqpgitfvaakfdGILGM 181
1T6G_B       89 sgaCAAGSls-hTRFVAnttdgskpvskvnvgVLAACapsklla-slprgstGVAGL 143
1ZAP_A       87 -gsSSQGTly-kDTVGFggvs--------iknQVLADvdst-------sidqGILGV 126
gi 85001307 164 --gSNVKGmyigDLVSFdtdedss--dlssffDYIGCvthesam-irsqitnGILGL 215

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