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(-) Description

Title :  CRYSTAL STRUCTURE OF MAPE1
 
Authors :  N. N. Noda, W. Adachi, F. Inagaki
Date :  20 Apr 16  (Deposition) - 29 Jun 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Tetrahedral Dodecamer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yamasaki, Y. Watanabe, W. Adachi, K. Suzuki, K. Matoba, H. Kirisako H. Kumeta, H. Nakatogawa, Y. Ohsumi, F. Inagaki, N. N. Noda
Structural Basis For Receptor-Mediated Selective Autophagy Of Aminopeptidase I Aggregates
Cell Rep V. 16 19 2016
PubMed-ID: 27320913  |  Reference-DOI: 10.1016/J.CELREP.2016.05.066

(-) Compounds

Molecule 1 - VACUOLAR AMINOPEPTIDASE 1
    Chains: A, B, C, D
    EC Number: 3.4.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 46-514
    Gene: APE1, API, LAP4, YSC1, YKL103C, YKL455
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: AMINOPEPTIDASE YSCI,LEUCINE AMINOPEPTIDASE IV,LAPIV, LYSOSOMAL AMINOPEPTIDASE III,POLYPEPTIDASE,VACUOLAR AMINOPEPTIDASE I

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:132 , ASP A:303 , ASP A:385 , ZN A:602 , HOH A:757 , HOH A:947binding site for residue ZN A 601
2AC2SOFTWAREASP A:303 , GLU A:340 , HIS A:479 , ZN A:601 , HOH A:757 , HOH B:925binding site for residue ZN A 602
3AC3SOFTWAREHOH A:788 , ASP B:303 , GLU B:340 , HIS B:479 , ZN B:602 , HOH B:752binding site for residue ZN B 601
4AC4SOFTWAREHIS B:132 , ASP B:303 , ASP B:385 , ZN B:601 , HOH B:752 , HOH B:911binding site for residue ZN B 602
5AC5SOFTWAREHIS C:132 , ASP C:303 , ASP C:385 , ZN C:602 , HOH C:752 , HOH C:955binding site for residue ZN C 601
6AC6SOFTWAREASP C:303 , GLU C:340 , HIS C:479 , ZN C:601 , HOH C:752 , HOH D:885binding site for residue ZN C 602
7AC7SOFTWAREHIS D:132 , ASP D:303 , ASP D:385 , ZN D:602 , HOH D:728 , HOH D:946binding site for residue ZN D 601
8AC8SOFTWAREHOH C:831 , ASP D:303 , GLU D:340 , HIS D:479 , ZN D:601 , HOH D:728binding site for residue ZN D 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JGF)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Thr A:197 -Pro A:198
2Gly A:217 -Pro A:218
3Asp A:303 -Asp A:304
4Thr B:197 -Pro B:198
5Gly B:217 -Pro B:218
6Asp B:303 -Asp B:304
7Thr C:197 -Pro C:198
8Gly C:217 -Pro C:218
9Asp C:303 -Asp C:304
10Thr D:197 -Pro D:198
11Gly D:217 -Pro D:218
12Asp D:303 -Asp D:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JGF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JGF)

(-) Exons   (0, 0)

(no "Exon" information available for 5JGF)

(-) Sequences/Alignments

Asymmetric Unit
   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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeee............ee..eeee....hhhhh...eeeeeeeee........eeeeee............hhhhhhhhh...........eee.........hhhhh......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhhh...eee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jgf A  47 HNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEF 511
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
                                                                                                                                                                                                                     234|                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                      240                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeee............ee..eeee....hhhhh...eeeeeeeeee......eeeeeee............hhhhhhhhh...........eee.........hhhhh......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhhh...eee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jgf B  47 HNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEF 511
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
                                                                                                                                                                                                                     234|                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                      240                                                                                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee..............eeeeeeee...eeeeeeee...hhhhh.eeeeee....eeee............ee..eeee....hhhhh...eeeeeeeee........eeeeee............hhhhhhhhh...........eee.........hhhhh......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee..ee.....hhhhh...........eeee.........hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jgf C  47 HNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEF 511
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511
                                                                                                                                                                                                                     234|                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                      240                                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee..............eeeeeeee...eeeeeeee...hhhhh.eeeeee....eeee............ee..eeee....hhhhh...eeeeeeeee........eeeeee............hhhhhhhhh...........eee...........hhhhh......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee..ee.....hhhhh...........eeee.........hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jgf D  47 HNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPDNEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEF 511
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509  
                                                                                                                                                                                                                      235|                                                                                                                                                                                                                                                                                
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  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 5JGF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JGF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JGF)

(-) Gene Ontology  (14, 14)

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  5jgf
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        AMPL_YEAST | P14904: 4r8f 5jge 5jh9 5jhc 5jm9

(-) Related Entries Specified in the PDB File

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