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(-) Description

Title :  CRYSTAL STRUCTURE OF PRAPE1
 
Authors :  N. N. Noda, W. Adachi, F. Inagaki
Date :  20 Apr 16  (Deposition) - 29 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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
    Gene: APE1, API, LAP4, YSC1, YKL103C, YKL455
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    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  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CAC8Ligand/IonCACODYLATE ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 24)
No.NameCountTypeFull Name
1CAC24Ligand/IonCACODYLATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:132 , ASP A:303 , ASP A:385 , ZN A:602 , CAC A:603 , HOH A:765binding site for residue ZN A 601
02AC2SOFTWAREASP A:303 , GLU A:340 , HIS A:479 , ZN A:601 , CAC A:603binding site for residue ZN A 602
03AC3SOFTWAREHIS A:132 , ASP A:303 , GLU A:339 , GLU A:340 , ASP A:385 , GLY A:454 , HIS A:479 , ZN A:601 , ZN A:602 , HIS B:210binding site for residue CAC A 603
04AC4SOFTWAREPRO A:214 , GLU A:216 , PRO A:218 , PHE A:219 , GLN A:224 , HOH B:747binding site for residue CAC A 604
05AC5SOFTWAREHIS B:132 , ASP B:303 , ASP B:385 , ZN B:602 , CAC B:603 , HOH B:852binding site for residue ZN B 601
06AC6SOFTWAREASP B:303 , GLU B:340 , HIS B:479 , ZN B:601 , CAC B:603binding site for residue ZN B 602
07AC7SOFTWAREHIS A:210 , HIS B:132 , ASP B:303 , GLU B:339 , GLU B:340 , ASP B:385 , GLY B:454 , HIS B:479 , ZN B:601 , ZN B:602binding site for residue CAC B 603
08AC8SOFTWAREHOH A:741 , LYS B:213 , PRO B:214 , GLU B:216 , PRO B:218 , PHE B:219 , GLN B:224binding site for residue CAC B 604
09AC9SOFTWAREHIS C:132 , ASP C:303 , ASP C:385 , ZN C:602 , CAC C:603 , HOH C:861binding site for residue ZN C 601
10AD1SOFTWAREASP C:303 , GLU C:340 , HIS C:479 , ZN C:601 , CAC C:603binding site for residue ZN C 602
11AD2SOFTWAREHIS C:132 , ASP C:303 , GLU C:339 , GLU C:340 , ASP C:385 , GLY C:454 , HIS C:479 , ZN C:601 , ZN C:602 , HIS D:210binding site for residue CAC C 603
12AD3SOFTWARELYS C:213 , PRO C:214 , GLU C:216 , PRO C:218 , PHE C:219 , GLN C:224 , HOH D:766binding site for residue CAC C 604
13AD4SOFTWAREHIS D:132 , ASP D:303 , ASP D:385 , ZN D:602 , CAC D:603 , HOH D:829binding site for residue ZN D 601
14AD5SOFTWAREASP D:303 , GLU D:340 , HIS D:479 , ZN D:601 , CAC D:603binding site for residue ZN D 602
15AD6SOFTWAREHIS C:210 , HIS D:132 , ASP D:303 , GLU D:339 , GLU D:340 , ASP D:385 , GLY D:454 , HIS D:479 , ZN D:601 , ZN D:602binding site for residue CAC D 603
16AD7SOFTWAREHOH C:804 , PRO D:214 , GLU D:216 , PRO D:218 , PHE D:219 , GLN D:224binding site for residue CAC D 604

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:43 -A:317
2B:43 -B:317
3C:43 -C:317
4D:43 -D:317

(-) 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 5JH9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JH9)

(-) Exons   (0, 0)

(no "Exon" information available for 5JH9)

(-) 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:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeee.......eeeeeeee....hhhhh...eeeeeeeee........eeeeee............hhhhhhhhh...........eee.......hhhhhh.......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eeeee..ee.....hhhhh...........eeee.........hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jh9 A  33 KEKKENENSWCILEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFG 512
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 ||    247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507     
                                                                                                                                                                                                                                   234|                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                    240                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:477
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeee.......eeeeeeee....hhhhh...eeeeeeeeee......eeeeeee............hhhhhhhhh...........eee.........hhhhh......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeee...........hhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eeeee..ee.....hhhhh...........eeee.........hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jh9 B  31 EEKEKKENENSWCILEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFG 512
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   ||  245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       
                                                                                                                                                                                                                                     234|                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                      240                                                                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeee............ee..eeee....hhhhh...eeeeeeeeee......eeeeeee............hhhhhhhhh...........eee.......hhhhhh.......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eeeee..ee.....hhhhh...........eeee.........hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jh9 C  35 KKENENSWCILEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFG 512
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234|      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   
                                                                                                                                                                                                                                 234|                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                  240                                                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee.....hhhhh.....eeeeeee...eeeeeee....hhhhh.eeeeee....eeee............ee..eeee....hhhhh...eeeeeeeeee......eeeeeee............hhhhhhhhh...........eee...........hhhhh......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhh.........eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eeeee..ee.....hhhhh...........eeee.........hhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jh9 D  35 KKENENSWCILEHNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAPHFGKPAEGPFDKEDQTIPVIGFPTPDNEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIKNNSRSGGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFG 512
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234||     247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507     
                                                                                                                                                                                                                                  235|                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                   239
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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 5JH9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JH9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JH9)

(-) Gene Ontology  (14, 14)

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  5jh9
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPL_YEAST | P14904: 4r8f 5jge 5jgf 5jhc 5jm9

(-) Related Entries Specified in the PDB File

5jgf 5jhc