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- PDB-3kv3: Crystal structure of C151S mutant of Glyceraldehyde-3-phosphate d... -

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Basic information

Entry
Database: PDB / ID: 3kv3
TitleCrystal structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH 1)from methicillin resistant Staphylococcus aureus MRSA252 complexed with NAD and G3P
ComponentsGAPDHGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / glycolysis
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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-PHOSPHOGLYCERIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMukherjee, S. / Dutta, D. / Saha, B. / Das, A.K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism.
Authors: Mukherjee, S. / Dutta, D. / Saha, B. / Das, A.K.
History
DepositionNov 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: GAPDH
Q: GAPDH
R: GAPDH
P: GAPDH
O: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Q: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
R: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
P: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,61712
Polymers145,2194
Non-polymers3,3988
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-62 kcal/mol
Surface area45950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.519, 104.490, 91.192
Angle α, β, γ (deg.)90.000, 108.030, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11O
21Q
31R
41P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 2 - 334 / Label seq-ID: 2 - 334

Dom-IDAuth asym-IDLabel asym-ID
1OA
2QB
3RC
4PD

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Components

#1: Protein
GAPDH / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 36304.699 Da / Num. of mol.: 4 / Mutation: C151S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MRSA252 / Gene: gap, gap1, gapA, gapA1, SAR0828 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q6GIL8, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE 3PG IS NOT PHOSPHOGLYCERIC ACID STRUCTURALLY. THE LIGAND BOUND IS THE GEM DI-OL FORM OF ...THE 3PG IS NOT PHOSPHOGLYCERIC ACID STRUCTURALLY. THE LIGAND BOUND IS THE GEM DI-OL FORM OF GLYCERALDEHYDE-3-PHOSPHATE (G3H).

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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: 2.14 Å3/Da / Density % sol: 42.46 % / Mosaicity: 0.944 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1 (M) Tris-HCl, pH 8.2, 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 22, 2009 / Details: Varimax mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→86.71 Å / Num. obs: 41759 / % possible obs: 98.8 % / Redundancy: 3.73 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.01 / Net I/σ(I): 9.7 / Scaling rejects: 1179
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.2 / Num. measured all: 15373 / Num. unique all: 4116 / Χ2: 1.17 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.69 Å21.35 Å
Translation2.69 Å21.35 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.8Ldata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H48

3h48
PDB Unreleased entry


Resolution: 2.5→21.35 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.838 / SU B: 22.248 / SU ML: 0.231 / SU R Cruickshank DPI: 0.256 / SU Rfree: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2100 5 %RANDOM
Rwork0.187 ---
obs0.19 41750 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 39.086 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0.44 Å2
2--2.53 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10124 0 220 232 10576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210492
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.98314248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56251332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86525.391460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.761151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1821556
X-RAY DIFFRACTIONr_chiral_restr0.0940.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027788
X-RAY DIFFRACTIONr_mcbond_it0.6611.56596
X-RAY DIFFRACTIONr_mcangle_it1.4162.510604
X-RAY DIFFRACTIONr_scbond_it3.80953896
X-RAY DIFFRACTIONr_scangle_it6.425103644
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
O1332TIGHT POSITIONAL0.060.05
Q1332TIGHT POSITIONAL0.060.05
R1332TIGHT POSITIONAL0.050.05
P1332TIGHT POSITIONAL0.060.05
O1191MEDIUM POSITIONAL0.070.5
Q1191MEDIUM POSITIONAL0.070.5
R1191MEDIUM POSITIONAL0.060.5
P1191MEDIUM POSITIONAL0.070.5
O1332TIGHT THERMAL0.130.5
Q1332TIGHT THERMAL0.140.5
R1332TIGHT THERMAL0.130.5
P1332TIGHT THERMAL0.120.5
O1191MEDIUM THERMAL0.162
Q1191MEDIUM THERMAL0.162
R1191MEDIUM THERMAL0.152
P1191MEDIUM THERMAL0.142
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 156 -
Rwork0.257 2897 -
all-3053 -
obs--97.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5397-0.0365-0.08891.11490.16821.0637-0.020.15520.1451-0.0533-0.0174-0.0982-0.0414-0.00140.03730.01060.00540.00780.06370.06690.077123.7984-0.73427.9683
21.1852-0.07190.07480.61650.14241.5062-0.0058-0.0993-0.0250.0429-0.0351-0.0850.07840.08340.04080.0158-0.0061-0.01150.01640.02460.041927.9493-21.122240.2879
31.0607-0.1544-0.01790.5976-0.20151.5771-0.0216-0.01340.07890.00130.01820.111-0.1404-0.28260.00350.02370.02080.00230.0581-0.0170.0551-6.7236-5.847234.7308
41.40450.23280.1920.64150.20942.4696-0.02680.1624-0.2411-0.0755-0.00410.0460.5682-0.27140.0310.1852-0.08240.00860.1115-0.06590.07743.5113-33.33589.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O1 - 334
2X-RAY DIFFRACTION2Q1 - 334
3X-RAY DIFFRACTION3R1 - 334
4X-RAY DIFFRACTION4P1 - 334

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