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- PDB-1tmm: Crystal structure of ternary complex of E.coli HPPK(W89A) with MG... -

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Basic information

Entry
Database: PDB / ID: 1tmm
TitleCrystal structure of ternary complex of E.coli HPPK(W89A) with MGAMPCPP and 6-Hydroxymethylpterin
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / CATALYTIC MECHANISM / FOLATE / HPPK / PTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / 6-HYDROXYMETHYLPTERIN / TERNARY COMPLEX / SUBSTRATE SPECIFICITY / PRODUCT RELEASE / ANTIMICROBIAL AGENT / DRUG DESIGN
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 6-HYDROXYMETHYLPTERIN / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBlaszczyk, J. / Li, Y. / Wu, Y. / Shi, G. / Ji, X. / Yan, H.
Citation
Journal: Biochemistry / Year: 2005
Title: Is the Critical Role of Loop 3 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase in Catalysis Due to Loop-3 Residues Arginine-84 and Tryptophan-89? Site-Directed ...Title: Is the Critical Role of Loop 3 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase in Catalysis Due to Loop-3 Residues Arginine-84 and Tryptophan-89? Site-Directed Mutagenesis, Biochemical, and Crystallographic Studies.
Authors: Li, Y. / Blaszczyk, J. / Wu, Y. / Shi, G. / Ji, X. / Yan, H.
#1: Journal: Structure / Year: 1999
Title: Crystal Structure of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, a Potential Target for the Development of Novel Antimicrobial Agents
Authors: Xiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X.
#2: Journal: Structure / Year: 2000
Title: Catalytic Center Assembly of Hppk as Revealed by the Crystal Structure of a Ternary Complex at 1.25 A Resolution
Authors: Blaszczyk, J. / Shi, G. / Yan, H. / Ji, X.
#3: Journal: J.Med.Chem. / Year: 2001
Title: Bisubstrate Analogue Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase: Synthesis and Biochemical and Crystallographic Studies
Authors: Shi, G. / Blaszczyk, J. / Ji, X. / Yan, H.
History
DepositionJun 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
B: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,74820
Polymers35,7032
Non-polymers2,04518
Water11,746652
1
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,96312
Polymers17,8511
Non-polymers1,11111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7858
Polymers17,8511
Non-polymers9347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.992, 47.392, 71.438
Angle α, β, γ (deg.)90.00, 104.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / HPPK / 6-hydroxymethyl-7 / 8-dihydropterin ...7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / HPPK / 6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK


Mass: 17851.402 Da / Num. of mol.: 2 / Mutation: W89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FOLK, B0142 / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase

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Non-polymers , 7 types, 670 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Details: MAGNESIUM CHLORIDE, FROM SIGMA, M2670
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Details: MAGNESIUM CHLORIDE, FROM SIGMA, M2670
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Details: SODIUM ACETATE, FROM SIGMA, S7670
#5: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Details: GLYCEROL, FROM SIGMA / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-HHR / 6-HYDROXYMETHYLPTERIN


Mass: 193.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O2 / Details: FROM SIGMA, M6517
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
Details: FROM SCHIRCKS LABORATORIES, CAT. NO. 11.421, SPONTANEUS CONVERSION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 24.5 %
Crystal growTemperature: 292 K / pH: 4.6
Details: PEG4000, MAGNESIUM CHLORIDE, ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2000 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 85986 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.037 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.8
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1Q0N

1q0n


Resolution: 1.25→30 Å / Num. parameters: 26939 / Num. restraintsaints: 34724 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
Details: FULL MATRIX LEAST-SQUARES PROCEDURE, WITH BLOCK OF PARAMETERS SET FOR EACH CYCLE OF INISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.164 4128 5.046 %RANDOM
obs0.132 -95 %-
all-81812 --
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 14 / Occupancy sum hydrogen: 2430 / Occupancy sum non hydrogen: 3294.5
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 126 652 3294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.089
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.09
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDTotal num. of bins used
1.25-1.320.185X-RAY DIFFRACTION9
1.32-1.40.154X-RAY DIFFRACTION9
1.4-1.490.13X-RAY DIFFRACTION9
1.49-1.60.111X-RAY DIFFRACTION9
1.6-1.740.099X-RAY DIFFRACTION9
1.74-1.930.094X-RAY DIFFRACTION9
1.93-2.260.094X-RAY DIFFRACTION9
2.26-3.030.095X-RAY DIFFRACTION9
3.03-300.132X-RAY DIFFRACTION9

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