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- PDB-4hnu: crystal structure of K442E mutant of S. aureus Pyruvate carboxylase -

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Basic information

Entry
Database: PDB / ID: 4hnu
Titlecrystal structure of K442E mutant of S. aureus Pyruvate carboxylase
ComponentsPyruvate carboxylase
KeywordsLIGASE
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2790 / pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. ...Arc Repressor Mutant, subunit A - #2790 / pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, A domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Cyclin A; domain 1 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Aldolase class I / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-BTI / : / Pyruvate carboxylase / Pyruvate carboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsYu, L.P.C. / Tong, L.
CitationJournal: Biochemistry / Year: 2013
Title: Characterizing the Importance of the Biotin Carboxylase Domain Dimer for Staphylococcus aureus Pyruvate Carboxylase Catalysis.
Authors: Yu, L.P. / Chou, C.Y. / Choi, P.H. / Tong, L.
History
DepositionOct 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Pyruvate carboxylase
B: Pyruvate carboxylase
C: Pyruvate carboxylase
D: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)525,54810
Polymers524,6724
Non-polymers8756
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-44 kcal/mol
Surface area153640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.569, 258.520, 126.898
Angle α, β, γ (deg.)90.00, 109.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate carboxylase


Mass: 131168.094 Da / Num. of mol.: 4 / Mutation: E442K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pycA / Production host: Escherichia coli (E. coli)
References: UniProt: Q99UY8, UniProt: A0A0H3JRU9*PLUS, pyruvate carboxylase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S
Sequence detailsTHE RESIDUES ARE NUMBERED ACCORDING TO THEIR EQUIVALENTS IN THE HUMAN PC SEQUENCE

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 294 K / pH: 7.5
Details: 200 mM ammonium tartrate and 20% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 115003 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CNSrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.886 / SU B: 41.003 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 5765 5 %RANDOM
Rwork0.194 ---
obs0.197 109041 98.4 %-
all-117000 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å21.01 Å2
2--1.23 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32397 0 46 0 32443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02233059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.96644697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.43854066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14624.7181598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.746155851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.49415196
X-RAY DIFFRACTIONr_chiral_restr0.0970.24969
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02125047
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_it0.8341.520305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.606232842
X-RAY DIFFRACTIONr_scbond_it2.472312754
X-RAY DIFFRACTIONr_scangle_it4.1914.511855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.16 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.331 829 -
Rwork0.245 15954 -
obs--99.52 %
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)
12.83061.064-0.82136.4182-2.25773.6998-0.0752-0.1816-0.15850.2419-0.1665-1.0574-0.31850.51210.24170.2806-0.0315-0.04220.17180.07630.406975.40451.7720.054
22.58451.0378-0.68114.4006-1.4315.4052-0.44320.31160.2366-0.80830.34491.1155-0.0463-0.73560.09830.5534-0.1623-0.39610.23830.10110.584648.2564.161-16.973
33.7253-0.89111.31844.2189-2.97777.6176-0.0673-0.59450.89470.8726-0.15420.6401-0.6754-0.75430.22151.0189-0.05620.37920.5663-0.27890.806562.725153.59859.928
42.52811.01480.1456.1703-1.53525.1970.2348-0.42190.26490.15450.0196-0.4956-0.24180.5767-0.25440.6271-0.23690.03660.6512-0.01830.556591.185156.74341.257
52.08620.3919-0.152.4552-0.01460.78460.00790.1371-0.23870.05680.0693-0.26490.16440.2339-0.07720.0804-0.01890.07580.3143-0.20820.294282.068115.218-20.537
61.69270.41190.61983.309-0.14022.52910.01280.1028-0.1207-0.0840.1523-0.52210.04050.8598-0.16510.35180.1427-0.01640.9317-0.08290.281581.59995.30962.246
71.84220.4271-0.69231.77741.07013.9599-0.1038-0.06270.1097-0.2683-0.06690.6144-0.0873-0.52290.17070.46560.0778-0.12590.5929-0.01430.53946.64876.71947.507
82.3484-0.48680.1561.50250.44651.8173-0.0530.038-0.20760.32220.06810.29690.0297-0.0084-0.01510.1354-0.0150.07320.02230.01230.287152.988140.647-5.132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 167
2X-RAY DIFFRACTION1A239 - 494
3X-RAY DIFFRACTION2C36 - 167
4X-RAY DIFFRACTION2C239 - 494
5X-RAY DIFFRACTION3D36 - 167
6X-RAY DIFFRACTION3D239 - 494
7X-RAY DIFFRACTION4B36 - 167
8X-RAY DIFFRACTION4B239 - 494
9X-RAY DIFFRACTION5A495 - 1093
10X-RAY DIFFRACTION6B495 - 1093
11X-RAY DIFFRACTION7C495 - 1093
12X-RAY DIFFRACTION8D495 - 1093

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