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- PDB-1cpy: SITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEA... -

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Basic information

Entry
Database: PDB / ID: 1cpy
TitleSITE-DIRECTED MUTAGENESIS ON (SERINE) CARBOXYPEPTIDASE Y FROM YEAST. THE SIGNIFICANCE OF THR 60 AND MET 398 IN HYDROLYSIS AND AMINOLYSIS REACTIONS
ComponentsSERINE CARBOXYPEPTIDASECarboxypeptidase D
KeywordsHYDROLASE (CARBOXYPEPTIDASE)
Function / homology
Function and homology information


phytochelatin biosynthetic process / fungal-type vacuole lumen / carboxypeptidase C / serine-type carboxypeptidase activity / fungal-type vacuole / zymogen activation / macroautophagy / endoplasmic reticulum / extracellular region / cytoplasm
Similarity search - Function
Helix Hairpins - #410 / Propeptide, carboxypeptidase Y / Carboxypeptidase Y pro-peptide / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Alpha/Beta hydrolase fold, catalytic domain ...Helix Hairpins - #410 / Propeptide, carboxypeptidase Y / Carboxypeptidase Y pro-peptide / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Alpha/Beta hydrolase fold, catalytic domain / Helix Hairpins / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsSorensen, S.B. / Raaschou-Nielsen, M. / Mortensen, U. / Remington, S.J. / Breddam, K.
Citation
Journal: J.Am.Chem.Soc. / Year: 1995
Title: Site-Directed Mutagenesis on (Serine) Carboxypeptidase Y from Yeast. The Significance of Thr 60 and met 398 in Hydrolysis and Aminolysis Reactions
Authors: Sorensen, S.B. / Raaschou-Nielsen, M. / Mortensen, U.H. / Remington, S.J. / Breddam, K.
#1: Journal: Biochemistry / Year: 1994
Title: 2.8 Angstroms Structure of Yeast Serine Carboxypeptidase
Authors: Endrizzi, J.A. / Breddam, K. / Remington, S.J.
History
DepositionMar 24, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, 5, 6, 7, 8, 9, 10 AND 11 OF S1A AND S1B ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE CARBOXYPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9034
Polymers47,2391
Non-polymers6643
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.000, 112.000, 112.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO 54 / 2: CIS PROLINE - PRO 96

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Components

#1: Protein SERINE CARBOXYPEPTIDASE / Carboxypeptidase D


Mass: 47239.293 Da / Num. of mol.: 1 / Mutation: E65A, E145A / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00729, carboxypeptidase C
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop / Details: Endrizzi, J.A., (1994) Biochemistry, 33, 11106.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-24 %PEG60001reservoir
20.3 M1reservoirNaOAc
30.05 M1reservoirNaCl
4100 mMimidazole/NaOH1reservoir
510 mg/mlCPD-Y1drop
60.1 M1dropNaCl
71 mMDTT1drop
820 mMcitrate/NaOH1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 14110 / % possible obs: 92 % / Observed criterion σ(I): 0 / Num. measured all: 48636 / Rmerge(I) obs: 0.072

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.18 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 42 38 3325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.023
X-RAY DIFFRACTIONt_angle_deg3.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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