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- PDB-2v8d: Crystal structure of mutant E159A of beta-alanine synthase from S... -

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Basic information

Entry
Database: PDB / ID: 2v8d
TitleCrystal structure of mutant E159A of beta-alanine synthase from Saccharomyces kluyveri
ComponentsBETA-ALANINE SYNTHASE
KeywordsHYDROLASE / DI-ZINC CENTER / AMIDOHYDROLASE
Function / homology
Function and homology information


beta-ureidopropionase / beta-ureidopropionase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-alanine synthase
Similarity search - Component
Biological speciesSACCHAROMYCES KLUYVERI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Yeast -Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements.
Authors: Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Yeast Beta-Alanine Synthase Shares a Structural Scaffold and Origin with Dizinc-Dependent Exopeptidases
Authors: Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Analysis of Beta-Alanine Synthase from the Yeast Saccharomyces Kluyveri
Authors: Dobritzsch, D. / Gojkovic, Z. / Andersen, B. / Piskur, J.
History
DepositionAug 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: BETA-ALANINE SYNTHASE
B: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1596
Polymers103,8982
Non-polymers2624
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-28.9 kcal/mol
Surface area40370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.117, 77.143, 108.228
Angle α, β, γ (deg.)90.00, 97.12, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A24 - 246
2116B24 - 246
1213A247 - 364
2213B247 - 364
1316A365 - 455
2316B365 - 455

NCS oper:
IDCodeMatrixVector
1given(-0.232, -0.972, -0.022), (-0.97, 0.23, 0.081), (-0.073, 0.04, -0.997)9.70329, 7.95056, 58.39275
2given(-0.233, -0.972, -0.039), (-0.971, 0.231, 0.063), (-0.052, 0.053, -0.997)9.85411, 8.21514, 57.56881
3given(-0.297, -0.955, 0.005), (-0.955, 0.297, -0.005), (0.004, -0.006, -1)10.36614, 7.80842, 56.94257

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Components

#1: Protein BETA-ALANINE SYNTHASE


Mass: 51948.773 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-455 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES KLUYVERI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q96W94, beta-ureidopropionase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 159 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 159 TO ALA
Sequence detailsTHE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION. THE LAST 20 ...THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION. THE LAST 20 AMINO ACIDS CORRESPOND TO THE C-TERMINAL HIS-TAG. E159 OF THE DEPOSITED SEQUENCE IS REPLACED BY ALANINE IN THIS MUTANT

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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: 2.45 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: TRISODIUM CITRATE, DIOXANE, ACETONE, DTT, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394
DetectorType: ADSC CCD / Detector: CCD / Date: May 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 43156 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R43

1r43


Resolution: 2.3→45.22 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.855 / SU ML: 0.238 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2195 5.1 %RANDOM
Rwork0.23 ---
obs0.232 40838 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.8 Å20 Å22.99 Å2
2---2.61 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6679 0 4 58 6741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226845
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9429277
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16824.528318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3531534
X-RAY DIFFRACTIONr_chiral_restr0.0780.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025272
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.23152
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24642
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2910.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3681.54399
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6326875
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.06632792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6164.52401
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
472tight positional0.030.05
2836loose positional1.35
472tight thermal0.080.5
2836loose thermal3.6410
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 139
Rwork0.284 2725
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)
11.44270.49610.14983.12140.26462.22070.10620.01950.42850.2037-0.04910.5981-0.3289-0.1591-0.057-0.38660.0438-0.1417-0.2181-0.05080.0317-25.5048-0.183654.3517
22.47730.22610.05543.51830.62812.38950.0338-0.17510.64270.1311-0.30560.6689-0.49770.10890.2718-0.1103-0.0251-0.0149-0.2391-0.11380.0968-19.134811.209758.3933
32.36631.331-1.72931.912-0.86021.34660.0143-0.1298-0.0895-0.1388-0.1663-0.13980.13080.20330.152-0.21880.0539-0.09-0.17690.0216-0.1485-1.7744-5.696644.6761
41.4797-0.02181.36522.8407-0.58592.8789-0.15360.16060.2364-0.4433-0.1373-0.5066-0.53350.07590.2910.49840.00790.30670.17790.10.022218.988734.29284.5062
58.218-4.3824-0.504713.90532.810317.9949-0.2256-0.1968-0.74760.0045-0.40981.35490.3609-0.45660.63540.0776-0.08220.0620.05280.06670.0010.467123.81555.4956
60.29880.2822-0.63431.544-0.76561.8743-0.11180.3412-0.0802-0.7190.0348-0.3980.08360.10470.0770.30980.02310.21470.1430.0482-0.048814.97110.54310.6355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 183
2X-RAY DIFFRACTION2A184 - 225
3X-RAY DIFFRACTION3A226 - 454
4X-RAY DIFFRACTION4B28 - 157
5X-RAY DIFFRACTION5B158 - 196
6X-RAY DIFFRACTION6B197 - 453

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