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- PDB-3ypi: ELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF... -

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Basic information

Entry
Database: PDB / ID: 3ypi
TitleELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF HISTIDINE-95
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHOGLYCOLOHYDROXAMIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsLolis, E. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1991
Title: Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95.
Authors: Komives, E.A. / Chang, L.C. / Lolis, E. / Tilton, R.F. / Petsko, G.A. / Knowles, J.R.
#1: Journal: Biochemistry / Year: 1990
Title: Crystallographic Analysis of the Complex between Triosephosphate Isomerase and 2-Phosphoglycolate at 2.5-Angstroms Resolution. Implications for Catalysis
Authors: Lolis, E. / Petsko, G.A.
#2: Journal: Biochemistry / Year: 1990
Title: Structure of Yeast Triosephosphate Isomerase at 1.9-Angstroms Resolution
Authors: Lolis, E. / Alber, T. / Davenport, R.C. / Rose, D. / Hartman, F.C. / Petsko, G.A.
#3: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1987
Title: Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a "Simple" Enzyme?
Authors: Alber, T.C. / Davenportjunior, R.C. / Giammona, D.A. / Lolis, E. / Petsko, G.A. / Ringe, D.
#4: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation
Authors: Alber, T. / Hartman, F.C. / Johnson, R.M. / Petsko, G.A. / Tsernoglou, D.
#5: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase
Authors: Alber, T. / Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D. / Rivers, P.S. / Wilson, I.A.
History
DepositionDec 31, 1990Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7154
Polymers53,3722
Non-polymers3422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-21 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.350, 83.970, 38.670
Angle α, β, γ (deg.)90.00, 99.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26686.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: 293 / Strain (production host): 293 / References: UniProt: P00942, triose-phosphate isomerase
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO6P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal grow
*PLUS
pH: 6.8 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
21.5 mMphosphoglycolohydroxamate11
3200 mMTris-HCl11
41 mM2-mercaptoethanol11
51 mMEDTA11

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.184 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 20 0 3784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.023
X-RAY DIFFRACTIONp_angle_d4
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 9635
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4

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