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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST AMINOPEPTIDASE 1 (APE1)
 
Authors :  M. -Y. Su, C. -I. Chang
Date :  02 Sep 14  (Deposition) - 12 Aug 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Peptidase, Cvt Pathway, Autophagy, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. -Y. Su, W. -H. Peng, M. -R. Ho, S. -C. Su, Y. -C. Chang, G. -C. Chen, C. -I. Chang
Structure Of Yeast Ape1 And Its Role In Autophagic Vesicle Formation
Autophagy 2015
PubMed-ID: 26208681  |  Reference-DOI: 10.1080/15548627.2015.1067363

(-) Compounds

Molecule 1 - VACUOLAR AMINOPEPTIDASE 1
    Chains: A, B, C, D
    EC Number: 3.4.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LAP4, APE1, API, YSC1, YKL103C, YKL455
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE S288C
    Organism Taxid: 559292
    Synonym: AMINOPEPTIDASE III, AMINOPEPTIDASE YSCI, LEUCINE AMINOPEPTIDASE IV, LAPIV, 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4R8F)

(-) Sites  (0, 0)

(no "Site" information available for 4R8F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R8F)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asp A:7 -Ile A:8
2Thr A:153 -Pro A:154
3Asp A:259 -Asp A:260
4Thr B:119 -Leu B:120
5Thr B:153 -Pro B:154
6Asp B:259 -Asp B:260
7Thr C:153 -Pro C:154
8Asp C:259 -Asp C:260
9Thr D:153 -Pro D:154
10Pro D:165 -His D:166
11Asp D:259 -Asp D:260
12Asn D:349 -Phe D:350

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R8F)

(-) Exons   (0, 0)

(no "Exon" information available for 4R8F)

(-) 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:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhhhhhhh...ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeeeeeee..eeeeeeeee....hhhhh...eeeeeeeee........eeeeee..................ee....hhhhhh.......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee.........hhhhh...........eeeee........hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.eeeeee..........eeee.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r8f A   3 HNYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLAKEDQTIPVEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL 470
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 ||    184|      205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395      |412       422       432       442       452       462        
                                                                                                                                                                                           164|    184|                                                                                                                                                                                                           402|                                                            
                                                                                                                                                                                            177     196                                                                                                                                                                                                            410                                                            


Chain B from PDB  Type:PROTEIN  Length:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeee....eeeeeee............eeeeeeeeee......eeeeeee.............ee....hhhhhh.......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee..........................eeee.........hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh.eeeeee..........eeee.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r8f B   4 NYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSQTIPVEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL 470
                                    13        23        33        43        53        63        73        83        93       107       117       127       137       147       157    || 184|      205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395      |412       422       432       442       452       462        
                                                                                                                            102|                                                    162| 184|                                                                                                                                                                                                           402|                                                            
                                                                                                                             107                                                     180  196                                                                                                                                                                                                            410                                                            


Chain C from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeee.......eeeeeeee....hhhhh...eeeeeeeee........eeeeee................eeee....hhhhhh.......hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhhhh........eeeeeee...........hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee.........hhhhh...........eeeee........hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh.eeeeee..........eeee.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r8f C   4 NYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLHFQTIPVINEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFPEVYLKNHFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL 470
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163|||    196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396     ||413       423       433       443       453       463       
                                                                                                                                                                                         163|||  185|                                                                                                                                                                                                            402|                                                            
                                                                                                                                                                                          166||   195                                                                                                                                                                                                             410                                                            
                                                                                                                                                                                           167|                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                            180                                                                                                                                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..ee...............eeeeeee...eeeeeee....hhhhh.eeeeee....eeeeeeeee.........eeeeee....hhhhh...eeeeeeeeee......eeeeeee.............................hhhhh......hhhhhhhhhhhhh.....eeeeeeeeee....eee.....eeee.....hhhhhhhhhhhhhhhhh........eeeeeee...........hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eeeee..ee............eeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.eeeeee.ee.......eeee.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r8f D   4 NYEDIAQEFIDFIYKNPTTYHVVSFFAELLDKHNFKYLSEKSNWQDSIGEDGGKFYTIRNGTNLSAFILGKNWRAEKGVGVIGSHVDALTVKLKPVSFKDTAEGYGRIAVAPYGGTLNELWLDRDLGIGGRLLYKKKGTNEIKSALVDSTPLPVCRIPSLPHFFDKEQTIPVEPPTDDEKKSPLFGKHCIHLLRYVAKLAGVEVSELIQMDLDLFDVQKGTIGGIGKHFLFAPRLDDRLCSFAAMIALICYAKDVNTEESDLFSTVTLYDNEEIGSLTRQGAKGGLLESVVERSSSAFTKKPVDLHTVWANSIILSADVNHLYNPNFFPVPNVGITLSLDPNGHMATDVVGTALVEELARRNGDKVQYFQIGTIGPSLASQTGARTIDLGIAQLSMHSIRAATGSKDVGLGVKFFNGFFKHWRSVYDEFGEL 470
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163| ||  |182 ||    203       213       223       233       243       253       263       273       283       293       303       313       323       333       343      |361       371       381       391       401||     418       428       438       448       458       468  
                                                                                                                                                                                         163| ||  || 184|                                                                                                                                                       350|                                        402|                                                            
                                                                                                                                                                                          165 ||  ||  196                                                                                                                                                        359                                         410                                                            
                                                                                                                                                                                            167|  ||                                                                                                                                                                                                                                                                        
                                                                                                                                                                                             175  ||                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                178|                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                 180
   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 4R8F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R8F)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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(no "Sites" information available for 4r8f)
 
  Cis Peptide Bonds
    Asn D:349 - Phe D:350   [ RasMol ]  
    Asp A:259 - Asp A:260   [ RasMol ]  
    Asp A:7 - Ile A:8   [ RasMol ]  
    Asp B:259 - Asp B:260   [ RasMol ]  
    Asp C:259 - Asp C:260   [ RasMol ]  
    Asp D:259 - Asp D:260   [ RasMol ]  
    Pro D:165 - His D:166   [ RasMol ]  
    Thr A:153 - Pro A:154   [ RasMol ]  
    Thr B:119 - Leu B:120   [ RasMol ]  
    Thr B:153 - Pro B:154   [ RasMol ]  
    Thr C:153 - Pro C:154   [ RasMol ]  
    Thr D:153 - Pro D:154   [ RasMol ]  
 
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  4r8f
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  AMPL_YEAST | P14904
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 Related Entries

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

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        AMPL_YEAST | P14904: 5jge 5jgf 5jh9 5jhc 5jm9

(-) Related Entries Specified in the PDB File

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