1DPJ - JenaLib

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:149 , LEU A:315 , MAN A:334 , HOH A:867 , HOH A:874 , HOH A:917 , HOH A:1113	BINDING SITE FOR RESIDUE BMA A 333
02	AC2	SOFTWARE	BMA A:333 , MAN A:336 , HOH A:1008 , HOH A:1098	BINDING SITE FOR RESIDUE MAN A 334
03	AC3	SOFTWARE	VAL A:134 , TYR A:138 , MAN A:334 , MAN A:335 , BMA A:337 , HOH A:831 , HOH A:862 , HOH A:877	BINDING SITE FOR RESIDUE MAN A 336
04	AC4	SOFTWARE	ASP A:159B , MAN A:336 , NAG A:338 , MAN A:341 , SO4 A:803 , HOH A:817 , HOH A:832 , HOH A:930 , HOH A:1008	BINDING SITE FOR RESIDUE BMA A 337
05	AC5	SOFTWARE	ASP A:131 , LYS A:132 , VAL A:134 , MAN A:335 , BMA A:337 , NAG A:339 , MAN A:340 , SO4 A:803 , HOH A:827 , HOH A:930 , HOH A:931 , HOH A:1106	BINDING SITE FOR RESIDUE NAG A 338
06	AC6	SOFTWARE	TYR A:64 , ASN A:67 , ASP A:100 , ASP A:131 , VAL A:133 , NAG A:338 , HOH A:847 , HOH A:931 , HOH A:1002 , HOH A:1062 , HOH A:1087	BINDING SITE FOR RESIDUE NAG A 339
07	AC7	SOFTWARE	BMA A:337	BINDING SITE FOR RESIDUE MAN A 341
08	AC8	SOFTWARE	GLN A:142 , MAN A:336 , NAG A:338 , MAN A:340 , SO4 A:803 , HOH A:1093	BINDING SITE FOR RESIDUE MAN A 335
09	AC9	SOFTWARE	LYS A:65 , LYS A:98 , VAL A:134 , MAN A:335 , NAG A:338 , HOH A:820 , HOH A:827 , HOH A:1007 , HOH A:1020 , HOH A:1131 , HOH A:1139	BINDING SITE FOR RESIDUE MAN A 340
10	BC1	SOFTWARE	TYR A:203 , GLY A:264 , ASN A:266 , HOH A:1086	BINDING SITE FOR RESIDUE NAG A 800
11	BC2	SOFTWARE	ARG A:185 , LYS A:193 , SER A:208 , HOH A:1082	BINDING SITE FOR RESIDUE SO4 A 801
12	BC3	SOFTWARE	SER A:279 , THR B:3 , ASP B:4 , HOH B:820	BINDING SITE FOR RESIDUE SO4 B 802
13	BC4	SOFTWARE	ASP A:159B , MAN A:335 , BMA A:337 , NAG A:338 , HOH A:1106 , HOH A:1124	BINDING SITE FOR RESIDUE SO4 A 803
14	BC5	SOFTWARE	LYS A:239 , GLN B:13 , LYS B:16	BINDING SITE FOR RESIDUE SO4 B 804

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (2, 2)

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:329
 aligned with CARP_YEAST | P07267 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:329
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396         
          CARP_YEAST     77 GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI  405
               SCOP domains d1dpja_ A: Acid protease                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1dpjA01 A:0-170 Acid Proteases                                                                                                                                                1dpjA02 A:171-325 Acid Proteases                                                                                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.eee...eeeeeeee....eeeeeeee.....eeee.....hhhhhh....hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhhhh.....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee..........eeeee...hhh.eeeeeeeee.......eeeeeeeee..eeee....eeee......eeehhhhhhhhhhhhh.ee.....eeehhhhhhhh..eeeee..eeeee.....eeee..eeee.eee.........eeeehhhhhh.eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PEPTIDASE_A1  PDB: A:14-323 UniProt: 91-402                                                                                                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 2 Exon 2.1  PDB: A:0-326 (gaps) UniProt: 1-405 [INCOMPLETE]                                                                                                                                                                                                                                                                                 Transcript 2
                1dpj A    0 GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI  326
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159|||    166       176       186       196       206   ||  217       227       237       247       257       267       277       287       297       307       317         
                                                                                                                                                                                         159A||                                                210|                                                                                                                  
                                                                                                                                                                                          159B|                                                 212                                                                                                                  
                                                                                                                                                                                           159C

Chain B from PDB  Type:PROTEIN  Length:29
 aligned with IPA3_YEAST | P01094 from UniProtKB/Swiss-Prot  Length:68

    Alignment length:29
                                    12        22         
          IPA3_YEAST      3 TDQQKVSEIFQSSKEKLQGDAKVVSDAFK   31
               SCOP domains d1dpjb_ B:                    SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE ----------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-31         Transcript 1
                1dpj B    3 TDQQKVSEIFQSSKEKLQGDAKVVSDAFK   31
                                    12        22

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 (2, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (17, 18)

Asymmetric Unit(hide GO term definitions)

Chain A (CARP_YEAST | P07267)

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:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0009267	cellular response to starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
	GO:0016237	lysosomal microautophagy	The transfer of cytosolic components into the lysosomal compartment by direct invagination of the lysosomal membrane without prior sequestration into an autophagosome. The engulfing membranes fuse, resulting in the lysosomal delivery of the cargo wrapped in a single membrane derived from the invaginated lysosomal membrane. In S. cerevisiae, the vacuole is the lysosomal compartment.
	GO:0032258	protein localization by the CVT pathway	A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0051603	proteolysis involved in cellular protein catabolic process	The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
cellular component
	GO:0000324	fungal-type vacuole	A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Chain B (IPA3_YEAST | P01094)

molecular function
	GO:0019828	aspartic-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of aspartic-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; the optimum reaction pH is below 5 due to an aspartic residue involved in the catalytic process.
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0007039	protein catabolic process in the vacuole	The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.
cellular component
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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		Glu A:293 - Pro A:294	[ RasMol ]
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		Thr A:22 - Pro A:23	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)