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- PDB-1ml3: Evidences for a flip-flop catalytic mechanism of Trypanosoma cruz... -

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Basic information

Entry
Database: PDB / ID: 1ml3
TitleEvidences for a flip-flop catalytic mechanism of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase, from its crystal structure in complex with reacted irreversible inhibitor 2-(2-phosphono-ethyl)-acrylic acid 4-nitro-phenyl ester
ComponentsGlyceraldehyde 3-phosphate dehydrogenase, glycosomal
KeywordsOXIDOREDUCTASE / protein covalent-inhibitor complex
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(3-FORMYL-BUT-3-ENYL)-PHOSPHONIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCastilho, M.S. / Pavao, F. / Oliva, G.
CitationJournal: Biochemistry / Year: 2003
Title: Evidence for the Two Phosphate Binding Sites of an Analogue of the Thioacyl Intermediate for the Trypanosoma cruzi Glyceraldehyde-3-phosphate Dehydrogenase-Catalyzed Reaction, from Its Crystal Structure.
Authors: Castilho, M.S. / Pavao, F. / Oliva, G. / Ladame, S. / Willson, M. / Perie, J.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN 2(2-phosphono-ethyl)-acrylic acid 4-nitro-phenyl ester underwent reaction with the ...HETEROGEN 2(2-phosphono-ethyl)-acrylic acid 4-nitro-phenyl ester underwent reaction with the protein. In chains B, C, and D, the product of the reaction, (3-FORMYL-BUT-3-ENYL)-PHOSPHONIC ACID, is bound to CYS 166. CYS 166 of chain A does not have this ligand bound. The ligand bound in alternate conformations for chains B and C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
B: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
C: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
D: Glyceraldehyde 3-phosphate dehydrogenase, glycosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,93310
Polymers156,4504
Non-polymers2,4836
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20270 Å2
ΔGint-116 kcal/mol
Surface area48310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.456, 85.259, 105.153
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde 3-phosphate dehydrogenase, glycosomal / GAPDH


Mass: 39112.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: gapdh / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P22513, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CYX / (3-FORMYL-BUT-3-ENYL)-PHOSPHONIC ACID


Mass: 164.096 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, CALCIUM ACETATE, EDTA, SODIUM AZIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoirpH7.3-7.5
30.1 Mcadmium acetate1reservoir
418 %PEG80001reservoir
51.0 mMEDTA1reservoir
61.0 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 48450 / % possible obs: 97.5 % / Redundancy: 2.77 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.73
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.47 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.57 / % possible all: 99
Reflection
*PLUS
% possible obs: 99 % / Redundancy: 2.8 % / Num. measured all: 134297
Reflection shell
*PLUS
% possible obs: 97.5 % / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE OF T.cruzi gGAPDH (Souza et al FEBES letters (1998), 424, 131-135)

Resolution: 2.5→20 Å
RfactorNum. reflection% reflection
Rfree0.2645 2455 -
Rwork0.1986 --
all-49486 -
obs-48450 97.5 %
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10984 0 182 695 11861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006174
X-RAY DIFFRACTIONc_angle_d1.22317
Refinement
*PLUS
% reflection Rfree: 3 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0063
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.22

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