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- PDB-5ukd: PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL... -

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Basic information

Entry
Database: PDB / ID: 5ukd
TitlePH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL TRANSFER TRANSITION STATE ANALOG
ComponentsURIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
KeywordsTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / NMP KINASE / PHOSPHORYL TRANSFER / TRANSITION STATE ANALOG COMPLEX
Function / homology
Function and homology information


pyrimidine nucleobase salvage / UMP/CMP kinase / CDP biosynthetic process / nucleotide salvage / : / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / UMP kinase activity / phosphotransferase activity, phosphate group as acceptor ...pyrimidine nucleobase salvage / UMP/CMP kinase / CDP biosynthetic process / nucleotide salvage / : / CMP kinase activity / dCMP kinase activity / Interconversion of nucleotide di- and triphosphates / UMP kinase activity / phosphotransferase activity, phosphate group as acceptor / UDP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
UMP-CMP kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / CYTIDINE-5'-MONOPHOSPHATE / UMP-CMP kinase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchlichting, I. / Reinstein, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog.
Authors: Schlichting, I. / Reinstein, J.
#1: Journal: Biochemistry / Year: 1997
Title: Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
Authors: Schlichting, I. / Reinstein, J.
#2: Journal: Biochemistry / Year: 1996
Title: Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: ...Title: Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.
Authors: Scheffzek, K. / Kliche, W. / Wiesmuller, L. / Reinstein, J.
#3: Journal: Febs Lett. / Year: 1995
Title: Crystallization and preliminary X-ray analysis of UMP/CMP-kinase from Dictyostelium discoideum with the specific bisubstrate inhibitor P1-(adenosine 5')-P5-(uridine 5')-pentaphosphate (UP5A).
Authors: Wiesmuller, L. / Scheffzek, K. / Kliche, W. / Goody, R.S. / Wittinghofer, A. / Reinstein, J.
#4: Journal: J.Biol.Chem. / Year: 1990
Title: cDNA-derived sequence of UMP-CMP kinase from Dictyostelium discoideum and expression of the enzyme in Escherichia coli.
Authors: Wiesmuller, L. / Noegel, A.A. / Barzu, O. / Gerisch, G. / Schleicher, M.
History
DepositionApr 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 12, 2014Group: Refinement description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.6Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8305
Polymers21,9711
Non-polymers8594
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.500, 77.500, 100.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE / UMP/CMP KINASE


Mass: 21970.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX2-214 / Gene: KCY_DICDI / Plasmid: PIMS5-CDUK-1 / Gene (production host): KCY_DICDI / Production host: Escherichia coli (E. coli) / References: UniProt: P20425, UMP/CMP kinase

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsALF3 IS A PLANAR TRIGONAL TRANSITION STATE ANALOG OF THE PHOSPHORYL GROUP BEING TRANSFERRED.

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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: 3.42 Å3/Da / Density % sol: 65 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8.8 / Method: vapor diffusion, hanging drop / Details: Wiesmuller, L., (1995) FEBS Lett., 363, 22.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
214 %(w/v)PEG33501drop
350 mMTris-HCl1drop
4100 mM1dropMgCl2
50.02 %sodium azide1drop
610 mMDTE1drop
728 %(w/v)PEG33501reservoir
8100 mMTris-HCl1reservoir
9200 mM1reservoirMgCl2
100.04 %sodium azide1reservoir
1120 mMDTE1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 1, 1998 / Details: MIRRORS
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 33934 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.02 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 136455
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.31

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKD

3ukd


Rfactor Rfree: 0.241 / Rfactor Rwork: 0.209 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 53 181 1771
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor obs: 0.209 / Rfactor Rfree: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg0.7
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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