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- PDB-1uke: UMP/CMP KINASE FROM SLIME MOLD -

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Basic information

Entry
Database: PDB / ID: 1uke
TitleUMP/CMP KINASE FROM SLIME MOLD
ComponentsURIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
KeywordsNUCLEOTIDE MONOPHOSPHATE KINASE / NMP KINASE / NUCLEOTIDE SPECIFICITY / PHOSPHORYL TRANSFER / BISUBSTRATE INHIBITOR
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
P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE / UMP-CMP kinase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / MIR (MIR) / Resolution: 2.2 Å
AuthorsScheffzek, K. / Kliche, W. / Wiesmueller, L. / Reinstein, J.
Citation
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.
#1: Journal: Protein Sci. / Year: 1995
Title: High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer
Authors: Abele, U. / Schulz, G.E.
#2: Journal: Structure / Year: 1995
Title: Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases
Authors: Vonrhein, C. / Schlauderer, G.J. / Schulz, G.E.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Substrate Specificity and Assembly of the Catalytic Center Derived from Two Structures of Ligated Uridylate Kinase
Authors: Muller-Dieckmann, H.J. / Schulz, G.E.
#4: 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.
#5: 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
DepositionJan 7, 1998Processing site: BNL
SupersessionApr 29, 1998ID: 1UKD
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)22,8883
Polymers21,9711
Non-polymers9182
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.500, 78.500, 101.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UP5 / P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE


Mass: 893.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N7O24P5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.56 Å3/Da / Density % sol: 65 % / Description: NUMBER OF MEASURED REFLECTIONS : 119529
Crystal growpH: 8 / Details: SEE REFERENCE 4, pH 8.
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: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 9, 1993 / Details: NICKEL COATED FRANKS DOUBLE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 16642 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.1
Reflection shellResolution: 2.2→2.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 119529

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR (MIR)
Starting model: ADENYLATE KINASE (PORCINE), PDB ENTRY 1ADK3

Resolution: 2.2→8 Å / σ(F): 0
Details: SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT ENTIRELY WELL DEFINED IN THE DENSITY AND WERE MODELLED BY STEREOCHEMISTRY: LYS 2, GLU 3, LYS 5, LYS 50, GLU 53, LYS 60, LYS 72, GLN 82, LYS 106, ...Details: SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT ENTIRELY WELL DEFINED IN THE DENSITY AND WERE MODELLED BY STEREOCHEMISTRY: LYS 2, GLU 3, LYS 5, LYS 50, GLU 53, LYS 60, LYS 72, GLN 82, LYS 106, PHE 108, SER 135, ARG 137, LYS 146. IN THE CASE OF ARG 137 DENSITY FOR MAIN CHAIN ATOMS IS DISCONNECTIVE.
RfactorNum. reflection% reflection
Rfree0.276 -10 %
Rwork0.215 --
obs0.215 15781 99.7 %
Displacement parametersBiso mean: 28 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 55 45 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.3

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