Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEAST. THE SIGNIFICANCE OF THR 60 AND MET 398 IN HYDROLYSIS AND AMINOLYSIS REACTIONS
 
Authors :  S. B. Sorensen, M. Raaschou-Nielsen, U. Mortensen, S. J. Remington, K.
Date :  24 Mar 95  (Deposition) - 15 Sep 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Carboxypeptidase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. B. Sorensen, M. Raaschou-Nielsen, U. H. Mortensen, S. J. Remington K. Breddam
Site-Directed Mutagenesis On (Serine) Carboxypeptidase Y From Yeast. The Significance Of Thr 60 And Met 398 In Hydrolysis And Aminolysis Reactions
J. Am. Chem. Soc. V. 117 5944 1995
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE CARBOXYPEPTIDASE
    ChainsA
    EC Number3.4.16.5
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:39 , ASN A:87 , HIS A:416BINDING SITE FOR RESIDUE NAG A 871
2AC2SOFTWAREARG A:165 , ASN A:166 , PHE A:167 , ASN A:168BINDING SITE FOR RESIDUE NAG A 1681
3AC3SOFTWAREASN A:368 , HOH A:450BINDING SITE FOR RESIDUE NAG A 3681
4CATUNKNOWNSER A:146 , ASP A:338 , HIS A:397 , ALA A:145NULL
5CBSUNKNOWNASN A:51 , GLY A:52 , ALA A:145 , HIS A:397NULL
6S1PUNKNOWNTHR A:60 , PHE A:64 , ALA A:65 , TYR A:256 , TYR A:269 , LEU A:272 , MET A:398NULL
7S1SUNKNOWNTYR A:147 , LEU A:178 , LEU A:245 , TRP A:312 , ILE A:340 , CYS A:341NULL

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:56 -A:298
2A:193 -A:207
3A:217 -A:240
4A:224 -A:233
5A:262 -A:268

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:53 -Pro A:54
2Gln A:95 -Pro A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_SER_SERPS00131 Serine carboxypeptidases, serine active site.CBPY_YEAST253-260  1A:142-149
2CARBOXYPEPT_SER_HISPS00560 Serine carboxypeptidases, histidine active site.CBPY_YEAST498-515  1A:387-404

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR297W1YMR297W.1XIII:861921-8635191599CBPY_YEAST1-5325321A:1-421421

(-) Sequences/Alignments

Asymmetric/Biological 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:421
 aligned with CBPY_YEAST | P00729 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:421
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531 
           CBPY_YEAST   112 KIKDPKILGIDPNVTQYTGYLDVEDEDKHFFFWTFESRNDPAKDPVILWLNGGPGCSSLTGLFFELGPSSIGPDLKPIGNPYSWNSNATVIFLDQPVNVGFSYSGSSGVSNTVAAGKDVYNFLELFFDQFPEYVNKGQDFHIAGESYAGHYIPVFASEILSHKDRNFNLTSVLIGNGLTDPLTQYNYYEPMACGEGGEPSVLPSEECSAMEDSLERCLGLIESCYDSQSVWSCVPATIYCNNAQLAPYQRTGRNVYDIRKDCEGGNLCYPTLQDIDDYLNQDYVKEAVGAEVDHYESCNFDINRNFLFAGDWMKPYHTAVTDLLNQDLPILVYAGDKDFICNWLGNKAWTDVLPWKYDEEFASQKVRNWTASITDEVAGEVKSYKHFTYLRVFNGGHMVPFDVPENALSMVNEWIHGGFSL 532
               SCOP domains d1cpya_ A: Serine carboxypeptidase II                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1cpyA01 A:1-180,A:253-421  [code=3.40.50.1820, no name defined]                                                                                                                     1cpyA02 A:181-252  [code=1.10.287.410, no name defined]                 1cpyA01 A:1-180,A:253-421  [code=3.40.50.1820, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eee.............eeeeeee....eeeeeeee..........eeeee........hhhh.....................hhhh.eee...........ee........hhhhhhhhhhhhhhhhh.hhh......eeeeee..hhhhhhhhhhhhh........eeeeeee.....hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhh.hhhhhh............hhhhhhhh...hhh...hhhhhhhhh....eeeeee.......hhhhhhhh........hhhhh...eeee......eeeeeeee..eeeeee......hhhh.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------CARBOXYP---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_SER_HI----------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-421 UniProt: 1-532 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1cpy A   1 KIKDPKILGIDPNVTQYTGYLDVEDEDKHFFFWTFESRNDPAKDPVILWLNGGPGCSSLTGLFFALGPSSIGPDLKPIGNPYSWNSNATVIFLDQPVNVGFSYSGSSGVSNTVAAGKDVYNFLELFFDQFPEYVNKGQDFHIAGASYAGHYIPVFASEILSHKDRNFNLTSVLIGNGLTDPLTQYNYYEPMACGEGGEPSVLPSEECSAMEDSLERCLGLIESCYDSQSVWSCVPATIYCNNAQLAPYQRTGRNVYDIRKDCEGGNLCYPTLQDIDDYLNQDYVKEAVGAEVDHYESCNFDINRNFLFAGDWMKPYHTAVTDLLNQDLPILVYAGDKDFICNWLGNKAWTDVLPWKYDEEFASQKVRNWTASITDEVAGEVKSYKHFTYLRVFNGGHMVPFDVPENALSMVNEWIHGGFSL 421
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPY_YEAST | P00729)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004185    serine-type carboxypeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0046938    phytochelatin biosynthetic process    The chemical reactions and pathways resulting in the formation of phytochelatins, any of a group of peptides that bind metals (Cd, Zn, Cu, Pb, Hg) in thiolate coordination complexes. The structure is of the type (gamma-glutamyl-cysteinyl)n-glycine, where n is 2 to 11.
    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.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    CAT  [ RasMol ]  +environment [ RasMol ]
    CBS  [ RasMol ]  +environment [ RasMol ]
    S1P  [ RasMol ]  +environment [ RasMol ]
    S1S  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:95 - Pro A:96   [ RasMol ]  
    Gly A:53 - Pro A:54   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1cpy
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CBPY_YEAST | P00729
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.16.5
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CBPY_YEAST | P00729
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CBPY_YEAST | P007291wpx 1ysc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CPY)