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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MOLECULAR MODELING OF THE ASPARTIC PROTEASE YAPSIN 1
 
Authors :  V. Olsen, K. Guruprasad, N. X. Cawley, H. -C. Chen, T. L. Blundell, Y. P. Loh
Date :  09 Apr 98  (Deposition) - 17 Jun 98  (Release) - 17 Jun 98  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B
Keywords :  Basic Residue Specific, Aspartic Protease, Pro-Hormone Processing, Complex (Aspartyl Protease/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Olsen, K. Guruprasad, N. X. Cawley, H. C. Chen, T. L. Blundell, Y. P. Loh
Cleavage Efficiency Of The Novel Aspartic Protease Yapsin 1 (Yap3P) Enhanced For Substrates With Arginine Residues Flanking The P1 Site: Correlation With Electronegative Active-Site Pockets Predicted By Molecular Modeling
Biochemistry V. 37 2768 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YAPSIN 1
    Cellular Location: PERIPLASM
    Chains: A
    EC Number: 3.4.23.-
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Synonym: YAP3P, YEAST ASPARTIC PROTEASE 3
 
Molecule 2 - CCK (18-26) PEPTIDE
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YPS)

(-) Sites  (0, 0)

(no "Site" information available for 1YPS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YPS)

(-) Cis Peptide Bonds  (4, 4)

Theoretical Model
No.Residues
1Thr A:20 -Pro A:21
2Ser A:147 -Asp A:148
3Gly A:199 -Ser A:200
4Asn A:313 -Leu A:314

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YPS)

(-) PROSITE Motifs  (2, 3)

Theoretical Model (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.YPS1_YEAST83-475  1A:12-319
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.YPS1_YEAST98-109
368-379		  2A:27-38
A:212-223

(-) Exons   (1, 1)

Theoretical Model (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR120C1YLR120C.1XII:388221-3865121710YPS1_YEAST1-5695691A:1-322 (gaps)407

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:311
 aligned with YPS1_YEAST | P32329 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:407
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       
           YPS1_YEAST    72 EEIIITNQQSFYSVDLEVGTPPQNVTVLVDTGSSDLWIMGSDNPYCSSNSMGSSRRRVIDKRDDSSSGGSLINDINPFGWLTGTGSAIGPTATGLGGGSGTATQSVPASEATMDCQQYGTFSTSGSSTFRSNNTYFSISYGDGTFASGTFGTDVLDLSDLNVTGLSFAVANETNSTMGVLGIGLPELEVTYSGSTASHSGKAYKYDNFPIVLKNSGAIKSNTYSLYLNDSDAMHGTILFGAVDHSKYTGTLYTIPIVNTLSASGFSSPIQFDVTINGIGISDSGSSNKTLTTTKIPALLDSGTTLTYLPQTVVSMIATELGAQYSSRIGYYVLDCPSDDSMEIVFDFGGFHINAPLSSFILSTGTTCLLGIIPTSDDTGTILGDSFLTNAYVVYDLENLEISMAQAR 478
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee....eeeeeeee............----------------------------------------------------------------------------....hhh.........eeeee.....eeeeeeeee.eee..eee..eeeeee.......eeee......................hhhh..-------.....eeeeee.......eeeee....hhh.....eeee.-------------..eeee.eeeee......eeeee..eeeee......eee.hhhhhhhhhhh...........eee........eeeee..eeeee.hhhh......eee..eee.hhh..eee.hhhh..eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------PEPTIDASE_A1  PDB: A:12-319 UniProt: 83-475                                                                                                                                                                                                                                                                                                                                                              --- PROSITE (1)
                PROSITE (2) --------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-322 (gaps) UniProt: 1-569 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                               Transcript 1
                 1yps A   1 EEIIITNQQSFYSVDLEVGTPPQNVTVLVDTGSSDLWIMGSD----------------------------------------------------------------------------GTFSTSGSSTFRSNNTYFSISYGDGTFASGTFGTDVLDLSDLNVTGLSFAVANETNSTMGVLGIGLPELEVTYSGSTASHSGKAYKYDNFP-------AIKSNTYSLYLNDSDAMHGTILFGAVDHSKYTGTLYTIPI-------------QFDVTINGIGISDSGSSNKTLTTTKIPALVDSGTTLTYLPQTVVSMIATELGAQYSSRIGYYVLDCPSDDSMEIVFDFGGFHINAPLSSFILSTGTTCLLGIIPTSDDTGTILGDSFLTNAYVVYDLENLEISMAQAR 322
                                    10        20        30        40 |       -         -         -         -         -         -         -        44        54        64        74        84        94       104       114       124        |-      |137       147       157       167     |   -       185       195       205       215       225       235       245       255       265       275       285       295       305       315       
                                                                    42                                                                           43                                                                                       133     134                                    173           185                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1yps B 323 RVSMIKNRR 331
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1YPS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YPS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YPS)

(-) Gene Ontology  (13, 13)

Theoretical Model(hide GO term definitions)
Chain A   (YPS1_YEAST | P32329)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0031505    fungal-type cell wall organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:0071432    peptide mating pheromone maturation involved in conjugation with cellular fusion    The formation of a mature peptide mating pheromone by proteolysis and/or modification of a peptide precursor, occurring in the context of conjugation with cellular fusion.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001402    signal transduction involved in filamentous growth    Relaying of environmental signals promoting filamentous growth.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0046658    anchored component of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  Cis Peptide Bonds
    Asn A:313 - Leu A:314   [ RasMol ]  
    Gly A:199 - Ser A:200   [ RasMol ]  
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