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- PDB-4ukd: UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM... -

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Basic information

Entry
Database: PDB / ID: 4ukd
TitleUMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE
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 / BERYLLIUM DIFLUORIDE / URIDINE-5'-DIPHOSPHATE / UMP-CMP kinase
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsSchlichting, I. / Reinstein, J.
Citation
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.
#1: 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.
#2: 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.
#3: 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
DepositionMay 20, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_conn_type / 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.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)22,8745
Polymers21,9711
Non-polymers9034
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.100, 78.100, 101.900
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, 111 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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-BF2 / BERYLLIUM DIFLUORIDE


Mass: 47.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsBEF2 LINKS THE TWO NUCLEOTIDE DIPHOSPHATES AND THUS STABILIZES THE SUBSTRATE COMPLEX.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.64 mMUmpKdicty11
20.8 mMADP11
30.8 mMCMP11or UMP
4100 mMTris-HCl11
530 mM11MgCl2
640 mMDTE11
70.8 mM11or BeCl2AlCl3
84 mM11NaF
9PEG400012

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→39 Å / Num. obs: 18420 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.084
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.366 / % possible all: 81
Reflection
*PLUS
Num. measured all: 136023
Reflection shell
*PLUS
% possible obs: 81 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2→39 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.212 -5 %
Rwork0.194 --
obs0.194 18420 95 %
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 55 107 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.07
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.07
LS refinement shell
*PLUS
% reflection Rfree: 5 %

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