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- PDB-1jqx: The R57A mutant of Lactococcus lactis dihydroorotate dehydrogenase A -

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Basic information

Entry
Database: PDB / ID: 1jqx
TitleThe R57A mutant of Lactococcus lactis dihydroorotate dehydrogenase A
Componentsdihydroorotate dehydrogenase A
KeywordsOXIDOREDUCTASE / Homodimer / alpha-beta barrel / flavoprotein / orotate complex / mutant enzyme
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : ...Dihydroorotate dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate Dehydrogenase A; chain A, domain 2 / Dihydroorotate Dehydrogenase A, chain A, domain 2 / Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase A (fumarate) / Dihydroorotate dehydrogenase A (fumarate)
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNorager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function
Authors: Norager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S.
#1: Journal: Biochemistry / Year: 1997
Title: Active site of dihydroorotate dehydrogenase A from Lactococcus lactis investigated by chemical modification and mutagenesis
Authors: Bjornberg, O. / Rowland, P. / Larsen, S. / Jensen, K.F.
#2: Journal: Protein Sci. / Year: 1998
Title: The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function
Authors: Rowland, P. / Bjornberg, O. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#3: Journal: Structure / Year: 1997
Title: The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis
Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#4: Journal: Protein Sci. / Year: 1996
Title: Purification and characterisation of dihydroorotate dehydrogenase A from Lactococcus lactis, crystallisation and preliminary X-ray diffraction studies of the enzyme
Authors: Nielsen, F.S. / Rowland, P. / Larsen, S. / Jensen, K.F.
History
DepositionAug 9, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dihydroorotate dehydrogenase A
B: dihydroorotate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,86211
Polymers68,3122
Non-polymers1,5509
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-50 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.350, 108.480, 66.120
Angle α, β, γ (deg.)90.00, 104.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe assymetric unit contains the biological homodimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein dihydroorotate dehydrogenase A


Mass: 34156.055 Da / Num. of mol.: 2 / Mutation: R57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Plasmid: pUHE23 / Production host: Escherichia coli (E. coli) / Strain (production host): SO6645
References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.3.1

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Non-polymers , 5 types, 731 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 6K, Na-acetate, TRIS-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 679947 / Num. obs: 80319 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 6.8 / Num. unique all: 3949 / % possible all: 97.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lactococcus lactis DHODA PDB ID 2DOR

2dor


Resolution: 1.7→25 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 8019 10.0255 %RANDOM
Rwork0.172 ---
all-79986 --
obs-79986 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8305 Å2 / ksol: 0.368323 e/Å3
Displacement parametersBiso mean: 19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 104 722 5632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.221 1367 10.3 %
Rwork0.203 11912 -
obs-11912 99.7 %

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