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Conserved domains on  [gi|676329712|gb|AIM38213|]
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clan AA aspartic protease [Sphingobacterium sp. ML3W]

Protein Classification

pepsin/retropepsin-like aspartic protease family protein( domain architecture ID 27721)

pepsin/retropepsin-like aspartic protease family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
pepsin_retropepsin_like super family cl11403
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ...
 17-123 8.07e-06

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).


The actual alignment was detected with superfamily member cd05483:

Pssm-ID: 472175  Cd Length: 96  Bit Score: 41.85  E-value: 8.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676329712  17 HILVEVMLFDTVHLMVLDTGASKTVFDKNQLEQIHAEQfQLETTDTLSTGLGtnTMQSFLIQIPIFKIQDWSIKNYKAAV 96
Cdd:cd05483    2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPL-TLGGKVTVQTANG--RVRAARVRLDSLQIGGITLRNVPAVV 78

                         90       100
                 ....*....|....*....|....*..
gi 676329712  97 LDLSSInyayeqmnlqPVIGVIGGDIL 123
Cdd:cd05483   79 LPGDAL----------GVDGLLGMDFL 95
 
Name Accession Description Interval E-value
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 17-123 8.07e-06

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 41.85  E-value: 8.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676329712  17 HILVEVMLFDTVHLMVLDTGASKTVFDKNQLEQIHAEQfQLETTDTLSTGLGtnTMQSFLIQIPIFKIQDWSIKNYKAAV 96
Cdd:cd05483    2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPL-TLGGKVTVQTANG--RVRAARVRLDSLQIGGITLRNVPAVV 78

                         90       100
                 ....*....|....*....|....*..
gi 676329712  97 LDLSSInyayeqmnlqPVIGVIGGDIL 123
Cdd:cd05483   79 LPGDAL----------GVDGLLGMDFL 95
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 20-99 1.58e-04

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 38.42  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676329712   20 VEVMLFDTVHLMVLDTGASKTVFDKNQLEQIHAEQFQLETTDTLSTGLGTNTMQsfLIQIPIFKIQDWSIKNYKAAVLDL 99
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGRVSAA--RVRLDSLRLGGLTLENVPALVLDL 78
 
Name Accession Description Interval E-value
retropepsin_like_bacteria cd05483
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ...
 17-123 8.07e-06

Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133150  Cd Length: 96  Bit Score: 41.85  E-value: 8.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676329712  17 HILVEVMLFDTVHLMVLDTGASKTVFDKNQLEQIHAEQfQLETTDTLSTGLGtnTMQSFLIQIPIFKIQDWSIKNYKAAV 96
Cdd:cd05483    2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPL-TLGGKVTVQTANG--RVRAARVRLDSLQIGGITLRNVPAVV 78

                         90       100
                 ....*....|....*....|....*..
gi 676329712  97 LDLSSInyayeqmnlqPVIGVIGGDIL 123
Cdd:cd05483   79 LPGDAL----------GVDGLLGMDFL 95
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
 20-99 1.58e-04

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 433378  Cd Length: 90  Bit Score: 38.42  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 676329712   20 VEVMLFDTVHLMVLDTGASKTVFDKNQLEQIHAEQFQLETTDTLSTGLGTNTMQsfLIQIPIFKIQDWSIKNYKAAVLDL 99
Cdd:pfam13650   1 VPVTINGKPVRFLVDTGASGTVISPSLAERLGLKVRGLAYTVRVSTAGGRVSAA--RVRLDSLRLGGLTLENVPALVLDL 78
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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