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- PDB-2cg8: The bifunctional dihydroneopterin aldolase 6-hydroxymethyl-7,8- d... -

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Basic information

Entry
Database: PDB / ID: 2cg8
TitleThe bifunctional dihydroneopterin aldolase 6-hydroxymethyl-7,8- dihydropterin synthase from Streptococcus pneumoniae
ComponentsDIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
KeywordsLYASE/TRANSFERASE / ALDOLASE / FOLATE BIOSYNTHESIS / PYROPHOSPHOKINASE / LYASE / MULTIFUNCTIONAL ENZYME / TRANSFERASE / LYASE-TRANSFERASE complex
Function / homology
Function and homology information


dihydroneopterin aldolase / dihydroneopterin aldolase activity / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding / metal ion binding
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK ...Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 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
Bifunctional folate synthesis protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGarcon, A. / Levy, C. / Derrick, J.P.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Bifunctional Dihydroneopterin Aldolase/6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase from Streptococcus Pneumoniae.
Authors: Garcon, A. / Levy, C. / Derrick, J.P.
History
DepositionFeb 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2006Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
B: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
C: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
D: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE


Theoretical massNumber of molelcules
Total (without water)124,5314
Polymers124,5314
Non-polymers00
Water00
1
A: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
B: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
C: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
D: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE

A: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
B: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
C: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE
D: DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE


Theoretical massNumber of molelcules
Total (without water)249,0628
Polymers249,0628
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)149.440, 149.440, 238.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRAA1 - 431 - 43
21METMETTHRTHRBB1 - 431 - 43
31METMETTHRTHRCC1 - 431 - 43
41METMETTHRTHRDD1 - 431 - 43
12VALVALASNASNAA51 - 12951 - 129
22VALVALASNASNBB51 - 12951 - 129
32VALVALASNASNCC51 - 12951 - 129
42VALVALASNASNDD51 - 12951 - 129
13ALAALASERSERAA140 - 156140 - 156
23ALAALASERSERBB140 - 156140 - 156
33ALAALASERSERCC140 - 156140 - 156
43ALAALASERSERDD140 - 156140 - 156
14ALAALAGLYGLYAA172 - 199172 - 199
24ALAALAGLYGLYBB172 - 199172 - 199
34ALAALAGLYGLYCC172 - 199172 - 199
44ALAALAGLYGLYDD172 - 199172 - 199
15LEULEUTYRTYRAA213 - 265213 - 265
25LEULEUTYRTYRBB213 - 265213 - 265
35LEULEUTYRTYRCC213 - 265213 - 265
45LEULEUTYRTYRDD213 - 265213 - 265

NCS oper:
IDCodeMatrixVector
1given(0.4934, 0.51, 0.7046), (0.5044, 0.4922, -0.7095), (-0.7086, 0.7054, -0.01443)0.3755, -0.402, -0.05502
2given(-0.2822, -0.7232, -0.6304), (-0.7139, -0.2806, 0.6416), (-0.6409, 0.6311, -0.4371)-57.07, -56.57, -0.2405
3given(-0.9501, -0.05956, -0.3061), (-0.04416, -0.946, 0.3211), (-0.3087, 0.3186, 0.8962)-57.26, -56.38, 0.5092
DetailsTHE QUATERNARY STRUCTURE WAS STUDIED BY LOPEZ ET AL 1993J BACTERIOL 175, 2214-2220, WHO CONCLUDED THAT IT IS ATETRAMER, BUT SUBSEQUENT STRUCTURES OF RELATED ALDOLASESFROM S. AUREUS AND M. TUBERCULOSIS HAVE ESTABLISHED THATAN OCTAMER IS MORE LIKELY.

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Components

#1: Protein
DIHYDRONEOPTERIN ALDOLASE 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN SYNTHASE / DIHYDRONEOPTERIN ALDOLASE / DHNA / 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE ...DIHYDRONEOPTERIN ALDOLASE / DHNA / 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE PYROPHOSPHOKINASE / 7 / 8-DIHYDRO-6-HYDROXYMETHYLPTERIN PYROPHOSPHOKINASE / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN PYROPHOSPHOKINASE / HPPK / PPPK


Mass: 31132.732 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P59657, dihydroneopterin aldolase, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
Sequence detailsGENBANK SEQUENCE DIFFERS FROM THAT REPORTED BY LOPEZ ET AL (1990) J BACT 172 4766 BY TWO MUTATIONS- ...GENBANK SEQUENCE DIFFERS FROM THAT REPORTED BY LOPEZ ET AL (1990) J BACT 172 4766 BY TWO MUTATIONS- V29I AND F86S. USED THE ORIGINAL SEQUENCE FOR THE STRUCTURE.

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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: 5.6 Å3/Da / Density % sol: 78 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.87→42 Å / Num. obs: 62341 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.4
Reflection shellResolution: 2.87→2.97 Å / Redundancy: 5.76 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
CNSphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NBU

1nbu


Resolution: 2.9→127 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / SU B: 24.764 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3059 5.1 %RANDOM
Rwork0.215 ---
obs0.216 57383 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2--1.34 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.9→127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 0 0 7968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.040.0228130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1641.97411018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.295966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.76624.828379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.571151482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8111538
X-RAY DIFFRACTIONr_chiral_restr0.1790.21271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026010
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2910.33503
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3630.55679
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.5425
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.379
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.73825038
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.57637949
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.25823523
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.28733069
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 1798 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.180.5
2Bmedium positional0.230.5
3Cmedium positional0.210.5
4Dmedium positional0.290.5
1Amedium thermal1.352
2Bmedium thermal1.522
3Cmedium thermal1.332
4Dmedium thermal1.482
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 207
Rwork0.322 4209
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)
11.71061.3979-0.65473.6593-0.95122.2302-0.05260.0548-0.1454-0.18630.0059-0.23650.26240.06850.0466-0.16130.03550.0483-0.1048-0.0358-0.1928-29.4719-48.5383-12.8108
23.01920.1684-0.61824.0684-0.63283.9613-0.15730.274-0.4263-0.58990.0773-0.21340.43550.09960.07990.00950.0164-0.0533-0.0878-0.0056-0.1243-49.9057-73.0863-16.7458
33.64350.8848-0.68771.8812-0.06861.61670.0716-0.2792-0.16110.2027-0.0188-0.03150.10130.0691-0.0528-0.0980.0357-0.0366-0.13410.0471-0.1923-30.3596-47.873213.658
42.8109-0.03770.14292.7433-1.12412.71930.0506-0.1162-0.0887-0.0428-0.066-0.1280.0694-0.00030.0154-0.07530.0263-0.0092-0.15810.0368-0.2054-49.453-73.596216.4347
51.0940.4815-0.43122.533-1.56682.6635-0.0036-0.0008-0.1075-0.11820.0022-0.25630.11240.21970.0015-0.15440.05520.0249-0.126-0.0688-0.1022-5.63-29.5164-7.5141
62.97830.9236-0.70194.7794-0.66432.7008-0.0830.0226-0.1414-0.1860.0119-0.61190.01920.58850.0711-0.1187-0.05590.02320.1727-0.01760.063820.4856-11.3331-6.9858
71.04380.8770.15714.60920.82332.0145-0.04640.0730.1141-0.09350.04320.195-0.2999-0.05540.0032-0.1418-0.00760.0256-0.07850.0311-0.1926-22.5922-12.8372-17.1371
82.57440.36190.44682.51060.37052.37940.05340.25120.3271-0.2949-0.0787-0.087-0.33860.20060.02540.0691-0.07790.08080.00330.0490.0189-0.17999.4605-22.7838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION1A51 - 120
3X-RAY DIFFRACTION2A121 - 159
4X-RAY DIFFRACTION2A170 - 200
5X-RAY DIFFRACTION2A211 - 267
6X-RAY DIFFRACTION3B1 - 44
7X-RAY DIFFRACTION3B49 - 120
8X-RAY DIFFRACTION4B121 - 160
9X-RAY DIFFRACTION4B169 - 200
10X-RAY DIFFRACTION4B209 - 267
11X-RAY DIFFRACTION5C1 - 120
12X-RAY DIFFRACTION6C121 - 159
13X-RAY DIFFRACTION6C170 - 200
14X-RAY DIFFRACTION6C210 - 267
15X-RAY DIFFRACTION7D1 - 44
16X-RAY DIFFRACTION7D49 - 120
17X-RAY DIFFRACTION8D121 - 158
18X-RAY DIFFRACTION8D170 - 200
19X-RAY DIFFRACTION8D207 - 267

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