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- PDB-2vom: Structural basis of human triosephosphate isomerase deficiency. M... -

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Basic information

Entry
Database: PDB / ID: 2vom
TitleStructural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation.
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / ALTERNATIVE SPLICING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / DISEASE MUTATION / PENTOSE SHUNT / PHOSPHOPROTEIN / GLUCONEOGENESIS / GLYCOLYSIS / ACETYLATION / POLYMORPHISM
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis / glycolytic process / gluconeogenesis / ubiquitin protein ligase binding / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRodriguez-Almazan, C. / Arreola-Alemon, R. / Rodriguez-Larrea, D. / Aguirre-Lopez, B. / de Gomez-Puyou, M.T. / Perez-Montfort, R. / Costas, M. / Gomez-Puyou, A. / Torres-Larios, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis of Human Triosephosphate Isomerase Deficiency: Mutation E104D is Related to Alterations of a Conserved Water Network at the Dimer Interface.
Authors: Rodriguez-Almazan, C. / Arreola-Alemon, R. / Rodriguez-Larrea, D. / Aguirre-Lopez, B. / De Gomez-Puyou, M.T. / Perez-Montfort, R. / Costas, M. / Gomez-Puyou, A. / Torres-Larios, A.
History
DepositionFeb 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)106,8014
Polymers106,8014
Non-polymers00
Water11,007611
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,4012
Polymers53,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-16.34 kcal/mol
Surface area18420 Å2
MethodPISA
2
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,4012
Polymers53,4012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-16.74 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)320.521, 47.288, 68.957
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2032-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.63124, 0.34401, -0.69512), (0.32328, -0.69798, -0.639), (-0.705, -0.62808, 0.32938)-8.66865, -4.32283, -6.54332
2given(-0.00865, 0.7749, -0.63203), (-0.99285, 0.06859, 0.09769), (0.11905, 0.62835, 0.76876)-27.01038, -37.60305, 36.36592
3given(0.7067, -0.12193, -0.69692), (0.59054, -0.44085, 0.67595), (-0.38966, -0.88926, -0.23955)-25.58899, -29.65629, 27.95633

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE / TIM


Mass: 26700.373 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-249 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P60174, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 105 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 105 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, GLU 105 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 105 TO ASP ENGINEERED RESIDUE IN CHAIN C, GLU 105 TO ASP ENGINEERED RESIDUE IN CHAIN D, GLU 105 TO ASP
Sequence detailsTHE STRUCTURE CORRESPONDS TO THE MUTANT E104D

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.58 % / Description: NONE
Crystal growpH: 8.5
Details: 100 MM TRIS PH 8.5, 20% PEG MME2000, 4% POLYPROPYLENE GLYCOL P400, 10 MM NICL2

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2007
Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→60.2 Å / Num. obs: 81960 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.11 / Net I/σ(I): 9.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.32 / % possible all: 93

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WYI

1wyi


Resolution: 1.85→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CHAIN D IS MORE DISORDERED THAN CHAINS A, B AND C ON RESIDUES 1 THIS IS PROBABLY DUE TO LACK OF CRYSTALLOGRAPHIC CONTACTS
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 4142 4.7 %RANDOM
Rwork0.2194 ---
obs0.2194 81958 92.8 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL / Bsol: 36.303 Å2 / ksol: 0.351707 e/Å3
Displacement parametersBiso mean: 23.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.265 Å20 Å20.146 Å2
2--0.45 Å20 Å2
3----1.715 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-50 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7372 0 0 611 7983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004809
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.25063
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.58
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.85→1.92 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 413 4.72 %
Rwork0.275 7727 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPARPROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPARWATER_REP.PARAM

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