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(-) Description

Title :  STRUCTURE OF NATIVE PROTEINASE A IN THE SPACE GROUP P21
 
Authors :  A. Gustchina, M. Li, L. H. Phylip, W. E. Lees, J. Kay, A. Wlodawer
Date :  18 Aug 00  (Deposition) - 31 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Proteinase A, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Gustchina, M. Li, L. H. Phylip, W. E. Lees, J. Kay, A. Wlodawer
An Unusual Orientation For Tyr75 In The Active Site Of The Aspartic Proteinase From Saccharomyces Cerevisiae.
Biochem. Biophys. Res. Commun. V. 295 1020 2002
PubMed-ID: 12127998  |  Reference-DOI: 10.1016/S0006-291X(02)00742-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SACCHAROPEPSIN
    ChainsA, B
    EC Number3.4.23.25
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPROTEINASE A

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG A:331 , HOH A:339BINDING SITE FOR RESIDUE BMA A 330
2AC2SOFTWAREASP A:132 , LYS A:133 , BMA A:330 , NAG A:332BINDING SITE FOR RESIDUE NAG A 331
3AC3SOFTWAREASN A:68 , THR A:70 , ASP A:101 , ASP A:132 , VAL A:134 , NAG A:331BINDING SITE FOR RESIDUE NAG A 332
4AC4SOFTWAREASP B:132 , LYS B:133 , VAL B:135 , NAG B:331 , HOH B:335BINDING SITE FOR RESIDUE NAG B 330
5AC5SOFTWAREASN B:68 , THR B:70 , ASP B:101 , ASP B:132 , VAL B:134 , NAG B:330BINDING SITE FOR RESIDUE NAG B 331
6AC6SOFTWARETYR A:207 , ASN A:269 , HOH A:371 , HOH A:383 , HOH A:436BINDING SITE FOR RESIDUE NAG A 333
7AC7SOFTWARETYR B:207 , GLY B:267 , ASN B:269 , HOH B:394 , HOH B:418BINDING SITE FOR RESIDUE NAG B 332

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:46 -A:51
2A:252 -A:285
3B:46 -B:51
4B:252 -B:285

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:23 -Pro A:24
2Glu A:296 -Pro A:297
3Gly A:299 -Pro A:300
4Thr B:23 -Pro B:24
5Glu B:296 -Pro B:297
6Gly B:299 -Pro B:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP_YEAST91-402
 
  2A:15-326
B:15-326
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP_YEAST106-117
 
291-302
 
  4A:30-41
B:30-41
A:215-226
B:215-226
Biological Unit 1 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP_YEAST91-402
 
  1A:15-326
-
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP_YEAST106-117
 
291-302
 
  2A:30-41
-
A:215-226
-
Biological Unit 2 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP_YEAST91-402
 
  1-
B:15-326
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP_YEAST106-117
 
291-302
 
  2-
B:30-41
-
B:215-226

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL154C1YPL154C.1XVI:260930-2597131218CARP_YEAST1-4054052A:1-329 (gaps)
B:1-329 (gaps)
329
329

(-) 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:325
 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 d1fmxa_ A: Acid protease                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1fmxA01 A:1-174 Acid Proteases                                                                                                                                                1fmxA02 A:175-328 Acid Proteases                                                                                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.eee...eeeeeeee....eeeeeeee.....eeee.....hhhhhh....hhhhh...eeeeeeee...----.eeeeeeeeeee..eeeeeeeeeeeee..hhhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeeee..........eeeee...hhh.eeeeeeeee.......eeeeeeeee....eeeeeeeeee......eeehhhhhhhhhhhhh.ee.....eeehhhhhhhh..eeeee..eeeeehhhhheeee..eeee.eee.........eeeehhhhhh.eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PEPTIDASE_A1  PDB: A:15-326 UniProt: 91-402                                                                                                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:1-329 (gaps) UniProt: 1-405 [INCOMPLETE]                                                                                                                                                                                                                                                                                 Transcript 1
                 1fmx A   1 GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQY----LEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI 329
                                    10        20        30        40        50        60        70     |   -|       90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320         
                                                                                                      76   81                                                                                                                                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:325
 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 d1fmxb_ B: Acid protease                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1fmxB01 B:1-174 Acid Proteases                                                                                                                                                1fmxB02 B:175-328 Acid Proteases                                                                                                                          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...hhhhh...eeeeeeee...----.eeeeeeeeeee..eeeeeeeeeeeee..hhhhhh....eeee..hhhhhhhhh.hhhhhhhhh......eeeeee..........eeeee...hhhh.....eeee.......eeeeeeeee..eeee....eeee......eeehhhhhhhhhhhh..ee.....ee.hhhhhhhh..eeeee..eeeeehhhhheee....eee.eee.........eeeehhhhhh.eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------PEPTIDASE_A1  PDB: B:15-326 UniProt: 91-402                                                                                                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:1-329 (gaps) UniProt: 1-405 [INCOMPLETE]                                                                                                                                                                                                                                                                                 Transcript 1
                 1fmx B   1 GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQY----LEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI 329
                                    10        20        30        40        50        60        70     |   -|       90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320         
                                                                                                      76   81                                                                                                                                                                                                                                                        

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CARP_YEAST | P072671dp5 1dpj 1fmu 1fq4 1fq5 1fq6 1fq7 1fq8 1g0v 2jxr

(-) Related Entries Specified in the PDB File

1fmu 1FMU CONTAINS THE SAME PROTEIN IN ANOTHER SPACE GROUP.