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- PDB-4bjh: Crystal Structure of the Aquifex Reactor Complex Formed by Dihydr... -

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Basic information

Entry
Database: PDB / ID: 4bjh
TitleCrystal Structure of the Aquifex Reactor Complex Formed by Dihydroorotase (H180A, H232A) with Dihydroorotate and Aspartate Transcarbamoylase with N-(phosphonacetyl)-L-aspartate (PALA)
Components
  • ASPARTATE CARBAMOYLTRANSFERASE
  • DIHYDROOROTASE
KeywordsHYDROLASE/TRANSFERASE / HYDROLASE-TRANSFERASE COMPLEX / PYRIMIDINE BIOSYNTHESIS
Function / homology
Function and homology information


allantoinase activity / purine nucleobase catabolic process / dihydroorotase / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / dihydroorotase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...allantoinase activity / purine nucleobase catabolic process / dihydroorotase / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / dihydroorotase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / cytoplasm
Similarity search - Function
Dihydroorotase / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Aspartate/ornithine carbamoyltransferase ...Dihydroorotase / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Chem-DOR / N-(PHOSPHONACETYL)-L-ASPARTIC ACID / PHOSPHATE ION / Aspartate carbamoyltransferase catalytic subunit / Dihydroorotase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEdwards, B.F.P. / Martin, P.D. / Grimley, E. / Vaishnav, A. / Fernando, R. / Brunzelle, J.S. / Cordes, M. / Evans, H.G. / Evans, D.R.
Citation
Journal: Bmc Biochem. / Year: 2013
Title: The Mononuclear Metal Center of Type-I Dihydroorotase from Aquifex Aeolicus.
Authors: Edwards, B.F. / Fernando, R. / Martin, P.D. / Grimley, E. / Cordes, M. / Vaishnav, A. / Brunzelle, J.S. / Evans, H.G. / Evans, D.R.
#1: Journal: Biochemistry / Year: 2009
Title: Dihydroorotase from the Hyperthermophile Aquifex Aeolicus is Activated by Stoichiometric Association with Aspartate Transcarbamoylase and Forms a One-Pot Reactor for Pyrimidine Biosynthesis.
Authors: Zhang, P. / Martin, P.D. / Purcarea, C. / Vaishnav, A. / Brunzelle, J.S. / Fernando, R. / Guy-Evans, H.I. / Evans, D.R. / Edwards, B.F.P.
History
DepositionApr 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: DIHYDROOROTASE
B: ASPARTATE CARBAMOYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,17621
Polymers87,4452
Non-polymers1,73019
Water8,017445
1
A: DIHYDROOROTASE
B: ASPARTATE CARBAMOYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)535,054126
Polymers524,67212
Non-polymers10,382114
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
Buried area53480 Å2
ΔGint-218.5 kcal/mol
Surface area163500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.152, 157.152, 233.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2028-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein DIHYDROOROTASE / / DHOASE


Mass: 50301.902 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria)
Description: GIFT FROM DRS KARL O. STETTER AND ROBERT HUBER, REGENSBURG UNIVERSITY, D-93053 REGENSBURG, GERMANY
Plasmid: PAAPYRC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66990, dihydroorotase
#2: Protein ASPARTATE CARBAMOYLTRANSFERASE / / ASPARTATE TRANSCARBAMYLASE / ATCASE


Mass: 37143.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria)
Description: GIFT FROM DRS KARL O. STETTER AND ROBERT HUBER, REGENSBURG UNIVERSITY, D-93053 REGENSBURG, GERMANY
Plasmid: PAAPYRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66726, aspartate carbamoyltransferase

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Non-polymers , 7 types, 464 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O4
#5: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10NO8P
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ba
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.17 Å3/Da / Density % sol: 61.2 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO- ...Details: THE CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN HANGING-DROPS. THE HETERO DODECAMER WAS BUFFER EXCHANGED INTO 10 MM HEPES, 1 MM TCEP PH 7.5, AT A FINAL PROTEIN CONCENTRATION OF 3.0 MG/ML. DHO-ATC SOLUTION (3-6 UL) WAS MIXED WITH 1 UL OF RESERVOIR SOLUTION (30% ETHYLENE GLYCOL) FOLLOWED BY 10% OF THE DROP VOLUME (V/V) OF 100 MM BARIUM CHLORIDE. THE FINAL CRYSTALLIZATION PH WAS 6.3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
DetectorType: MARRESEARCH MAR300 / Detector: CCD / Date: May 29, 2009 / Details: BE LENSES
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→77.85 Å / Num. obs: 53365 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
ARP/wARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D6N

3d6n


Resolution: 2.2→77.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.853 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL ATOMS IN RESIDUES MET1-ASP422 IN DHO AND RESIDUES MET1- -THR291 IN ATC ARE INCLUDED IN THE REFINEMENT AT FULL WEIGHT. ALL RESIDUES ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL ATOMS IN RESIDUES MET1-ASP422 IN DHO AND RESIDUES MET1- -THR291 IN ATC ARE INCLUDED IN THE REFINEMENT AT FULL WEIGHT. ALL RESIDUES EXCEPT MET1, LEU2, AND GLU42 IN DHO AND MET1 IN ATC HAVE ELECTRON DENSITY AT 1 SIGMA FOR ALL MAIN CHAIN ATOMS. RESIDUES LYS3, ILE5, LYS7, LYS33, LEU39, VAL40, GLU42, ALA43, LYS49, AND ALA373 IN THE COMPOSITE DOMAIN OF DHO, WHICH COMPRISES RESIDUES 1-55 PLUS 366-422, HAVE NO DENSITY AT 1 SIGMA FOR THEIR SIDE CHAINS, ALTHOUGH ALL OF THEM HAVE ELECTRON DENSITY FOR ONE OR MORE SIDE CHAIN ATOMS AT 0.5 SIGMA. SEVEN OF THESE RESIDUES OCCUR WITHIN THE LEAST DEFINED SEGMENT OF THE DHO SUBUNIT, ILE24-LYS49.
RfactorNum. reflection% reflectionSelection details
Rfree0.20304 2846 5.1 %RANDOM
Rwork0.16066 ---
obs0.16282 53365 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.256 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.14 Å20 Å2
2---0.27 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 84 445 6151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225795
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9887800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83724.449245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.736151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0941532
X-RAY DIFFRACTIONr_chiral_restr0.1040.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214252
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7381.53543
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42325753
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.58832252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1844.52047
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 204 -
Rwork0.243 3906 -
obs--100 %
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)
10.8481-0.0388-0.00510.52930.03070.9203-0.0166-0.04650.25610.0455-0.0072-0.0047-0.3114-0.05610.02380.25830.0094-0.01760.0205-0.03420.1527-0.606-44.98-30.026
20.04840.0519-0.01270.0906-0.00890.0279-0.0040.0003-0.04330.0507-0.0315-0.01350.01-0.03550.03550.1985-0.0318-0.02150.1062-0.04560.1584-0.468-53.785-29.824
313.5641-23.980611.512742.4099-18.9365169.8844-0.93870.43820.15651.7246-0.6816-0.2477-2.42774.01061.62030.6555-0.22570.17810.4082-0.00920.53430.078-56.996-26.439
40.88120.1087-0.11360.5023-0.06080.49250.0068-0.09820.04070.0759-0.0285-0.0266-0.080.0570.02170.1537-0.027-0.04710.1459-0.03790.078817.07-75.444-1.747
51.9926-4.53650.460717.0626-0.36980.17520.1595-0.1572-0.26380.0909-0.0537-0.06850.074-0.0887-0.10580.2329-0.0536-0.04240.4382-0.11730.199415.215-81.003-5.488
60.45631.21243.09094.64132.938341.45420.03120.06750.26130.07220.08420.91152.84150.1555-0.11540.2520.0002-0.02920.26630.04511.1548-0.003-90.738-8.148
75.53341.232113.13711.44472.188831.341-1.772-1.53271.7141-0.2858-0.4602-1.7123-0.8324-3.82242.23220.23340.0218-0.11320.6809-0.1773.97540.26-90.94-4.52
84.30942.27780.96232.62753.8468.1195-0.141-0.09230.4914-0.16540.20540.3342-0.39360.8114-0.06450.27910.05280.05710.29030.00740.791111.197-60.8967.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 422
2X-RAY DIFFRACTION2A423
3X-RAY DIFFRACTION3A425
4X-RAY DIFFRACTION4B1 - 291
5X-RAY DIFFRACTION5B292
6X-RAY DIFFRACTION6B295
7X-RAY DIFFRACTION7B296
8X-RAY DIFFRACTION8B297

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