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- PDB-5z79: Crystal Structure Analysis of the HPPK-DHPS in complex with substrates -

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Basic information

Entry
Database: PDB / ID: 5z79
TitleCrystal Structure Analysis of the HPPK-DHPS in complex with substrates
ComponentsHydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
KeywordsTRANSFERASE / Bifunctional / Malaria Pterin / Substrates
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase / Dihydropteroate synthase signature 2. / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
5'-DEOXYADENOSINE / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / 4-AMINOBENZOIC ACID / PTERINE / : / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsManickam, Y. / Karl, H. / Sharma, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase-dihydropteroate synthase fromPlasmodium vivaxsheds light on drug resistance
Authors: Yogavel, M. / Nettleship, J.E. / Sharma, A. / Harlos, K. / Jamwal, A. / Chaturvedi, R. / Sharma, M. / Jain, V. / Chhibber-Goel, J. / Sharma, A.
History
DepositionJan 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.2Dec 18, 2019Group: Data collection / Structure summary / Category: entity / reflns / reflns_shell
Item: _entity.formula_weight / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 25, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Mar 12, 2025Group: Database references / Structure summary
Category: pdbx_database_related / pdbx_entry_details / struct_keywords
Item: _pdbx_entry_details.has_protein_modification / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
B: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
C: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
D: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
E: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
F: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,11030
Polymers494,9056
Non-polymers5,20424
Water3,909217
1
A: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
B: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,89310
Polymers164,9682
Non-polymers1,9248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-34 kcal/mol
Surface area49430 Å2
MethodPISA
2
C: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
D: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,08012
Polymers164,9682
Non-polymers2,11210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-42 kcal/mol
Surface area50110 Å2
MethodPISA
3
E: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
F: Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,1368
Polymers164,9682
Non-polymers1,1686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-41 kcal/mol
Surface area49060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.049, 113.892, 172.387
Angle α, β, γ (deg.)90.00, 94.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase, putative


Mass: 82484.242 Da / Num. of mol.: 6 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
References: UniProt: A0A1K9YMY7, UniProt: A5JZS1*PLUS, dihydropteroate synthase, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase

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Non-polymers , 7 types, 241 molecules

#2: Chemical
ChemComp-HH2 / 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE / [PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE


Mass: 353.123 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H9N5O8P2
#3: 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 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-PAB / 4-AMINOBENZOIC ACID


Mass: 137.136 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H7NO2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-PE0 / PTERINE


Mass: 163.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5N5O
#7: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
Sequence detailsThe used cloned protein sequence has Ala383.

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.2M Potassium citrate tribasic monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2017
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.79→49.82 Å / Num. obs: 129475 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.9 / Net I/σ(I): 4.5
Reflection shellResolution: 2.79→2.84 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5799 / CC1/2: 0.2 / % possible all: 90.41

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PHASERphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYE

1eye


Resolution: 2.9→49.82 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.84 / SU B: 41.744 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28542 2006 1.7 %RANDOM
Rwork0.24186 ---
obs0.24263 114185 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.362 Å2
Baniso -1Baniso -2Baniso -3
1--6.79 Å20 Å2-1.17 Å2
2--2.35 Å2-0 Å2
3---4.47 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28365 0 342 217 28924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01929743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0228791
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.98140171
X-RAY DIFFRACTIONr_angle_other_deg0.837366227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77553460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02324.1581426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.032155557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.18915179
X-RAY DIFFRACTIONr_chiral_restr0.0890.24488
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0232598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026813
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 144 -
Rwork0.354 8347 -
obs--99.55 %
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)
11.69370.58450.50631.20710.31580.9137-0.01380.09110.0245-0.01670.0718-0.06520.01980.0197-0.05790.5970.0435-0.12680.26430.02160.0402-8.575-12.226-15.254
22.1281-0.62461.00891.3883-0.53621.77590.1670.0938-0.1884-0.1431-0.02870.23290.0082-0.2061-0.13820.7637-0.0428-0.1590.5586-0.01630.0674-47.642-12.64-58.909
31.4367-0.18560.60820.8258-0.43671.48890.0537-0.0982-0.03070.0848-0.04110.0323-0.01780.0166-0.01250.58130.0033-0.15590.1890.00790.0463-37.8925.9960.584
42.69980.5214-0.20630.6666-0.09770.3941-0.00990.1588-0.0978-0.039-0.01280.0620.1101-0.00210.02270.67820.0426-0.16750.2412-0.01360.0609-89.51736.152-25.58
52.5638-0.19720.21970.63310.06010.9403-0.09350.1102-0.0066-0.1240.0884-0.0328-0.03140.13480.00510.8346-0.0781-0.21980.39710.00350.066220.41534.205-70.643
61.10460.22680.40161.18030.58571.53960.02530.10680.0354-0.0155-0.10710.0388-0.0154-0.22510.08180.6984-0.0432-0.19060.54150.0180.0569-31.03521.131-95.36
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 716
2X-RAY DIFFRACTION2B11 - 717
3X-RAY DIFFRACTION3C10 - 716
4X-RAY DIFFRACTION4D12 - 716
5X-RAY DIFFRACTION5E10 - 716
6X-RAY DIFFRACTION6F11 - 716

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