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- PDB-1f76: ESCHERICHIA COLI DIHYDROOROTATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1f76
TitleESCHERICHIA COLI DIHYDROOROTATE DEHYDROGENASE
ComponentsDihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE / MONOMER / ALPHA-BETA-BARREL / FMN BINDING DOMAIN / OROTATE COMPLEX
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / FMN binding / membrane / plasma membrane / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 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 ...Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FORMIC ACID / OROTIC ACID / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsNorager, S. / Jensen, K.F. / Bjornberg, O. / Larsen, S.
Citation
Journal: Structure / Year: 2002
Title: E. coli Dihydroorotate Dehydrogenase Reveals Structural and Functional Distinction between different classes of dihydroorotate dehydrogenases
Authors: Norager, S. / Jensen, K.F. / Bjornberg, O. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-ray Studies of Membrane-associated Escherichia coli Dihydroorotate Dehydrogenase.
Authors: Rowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
#2: Journal: Biochemistry / Year: 1999
Title: The Activity of Escherichia coli Dihydroorotate Dehydrogenase is Dependent on a Conserved Loop Identified by Sequence Homology, Mutagenesis and Limited Proteolysis.
Authors: Bjornberg, O. / Gruner, A.-C. / Roepstorff, P. / Jensen, K.F.
#3: Journal: Flavins and Flavoproteins,Proc.13th Int.Symp. / Year: 1999
Title: The Dihydroorotate Dehydrogenases of Escherichia coli and Lactococcus Lactis Represent Two Distinct Families of the Enzyme.
Authors: Bjornberg, O. / Jensen, K.F. / Gruner, A.-C. / Ottosen, M. / Sorensen, P. / Rowland, P. / Norager, S. / Larsen, S.
#4: Journal: Flavins and Flavoproteins,Proc.13th Int.Symp. / Year: 1999
Title: Reduction Reactions of Two Dihydroorotate Dehydrogenases.
Authors: Palfey, B. / Bjornberg, O. / Jensen, K.F.
History
DepositionJun 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 12, 2014Group: Source and taxonomy / Version format compliance
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone)
B: Dihydroorotate dehydrogenase (quinone)
D: Dihydroorotate dehydrogenase (quinone)
E: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,24919
Polymers148,5874
Non-polymers2,66215
Water18,7901043
1
A: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9154
Polymers37,1471
Non-polymers7693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7415
Polymers37,1471
Non-polymers5944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8515
Polymers37,1471
Non-polymers7044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7415
Polymers37,1471
Non-polymers5944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.700, 119.700, 295.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer. The Biological Assembly is a Monomer.

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Components

#1: Protein
Dihydroorotate dehydrogenase (quinone) / DHOdehase / DHOD / DHODase / Dihydroorotate oxidase


Mass: 37146.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pyrD, b0945, JW0928 / Plasmid: PAG1 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A7E1, dihydroorotate dehydrogenase (quinone)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 156.096 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1043 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 3.3 to 3.7 M Na-formate, 0.1 M Na-acetate, 25 mM b-OG, 12-15 mg/ml protein, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mM1droppH7.0NaH2PO4
20.100 mMEDTA1drop
31 mMdithiothreitol1drop
410 %glycerol1drop
53.3-3.7 Msodium formate1reservoir
60.1 Msodium acetate1reservoirpH3.5-4.5
725 mMbeta-octylglucoside prior1reservoir
812-15 mg/mlprotein1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 1999
RadiationProtocol: MULTIPLE ANOMALOUS DIFFRACTION / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 75583 / Num. obs: 920967 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.1
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.334 / Num. unique all: 3137 / % possible all: 84.6
Reflection
*PLUS
Num. obs: 75583 / % possible obs: 98 % / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 84.6 % / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure Solved from a MAD Data Set Collected on the Se-methionine Substituted Enzyme
RfactorNum. reflection% reflectionSelection details
Rfree0.217 7460 10.1 %RANDOM
Rwork0.177 ---
all-73916 --
obs-73916 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.1302 Å2 / ksol: 0.336959 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10344 0 181 1043 11568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d22.4
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d0.95
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.351.5
X-RAY DIFFRACTIONo_mcangle_it2.142
X-RAY DIFFRACTIONo_scbond_it2.382
X-RAY DIFFRACTIONo_scangle_it3.262.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 1157 9.9 %
Rwork0.219 10481 -
obs--94.6 %
Refinement
*PLUS
Rfactor Rfree: 0.217 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.26
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg22.4
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.219

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