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PDBsum entry 4ukd
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protein ligands metals links
Transferase PDB id
4ukd

 

 

 

 

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Contents
Protein chain
191 a.a. *
Ligands
ADP-UDP-BF2
Metals
_MG
Waters ×107
* Residue conservation analysis
PDB id:
4ukd
Name: Transferase
Title: Ump/cmp kinase from slime mold complexed with adp, udp, beryllium fluoride
Structure: Uridylmonophosphate/cytidylmonophosphate kinase. Chain: a. Synonym: ump/cmp kinase. Engineered: yes
Source: Dictyostelium discoideum. Organism_taxid: 44689. Strain: ax2-214. Gene: kcy_dicdi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.194     R-free:   0.212
Authors: I.Schlichting,J.Reinstein
Key ref:
I.Schlichting and J.Reinstein (1997). Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative. Biochemistry, 36, 9290-9296. PubMed id: 9280438 DOI: 10.1021/bi970974c
Date:
20-May-97     Release date:   20-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20425  (KCY_DICDI) -  UMP-CMP kinase from Dictyostelium discoideum
Seq:
Struc: 		195 a.a.
191 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.14  - UMP/CMP kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. CMP + ATP = CDP + ADP
2. dCMP + ATP = dCDP + ADP
3. UMP + ATP = UDP + ADP
CMP
 + ATP
 =
CDP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ ADP
dCMP
 + ATP
 =
dCDP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ ADP
UMP
 + ATP
 =
UDP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+
ADP
Bound ligand (Het Group name = UDP)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi970974c Biochemistry 36:9290-9296 (1997)
PubMed id: 9280438  
 
 
Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
I.Schlichting, J.Reinstein.
 
  ABSTRACT  
 
UMP/CMP kinase from Dictyostelium discoideum (UmpKdicty) catalyzes the specific transfer of the terminal phosphate of ATP to UMP or CMP. Crystal structures of UmpKdicty with substrates and the transition state analogs AlF3 or BeF2 that lock UmpKdicty in active conformations were solved. The positions of the catalytic Mg2+ and the highly conserved lysine of the P loop are virtually invariant in the different structures. In contrast, catalytic arginines move to stabilize charges that develop during this reaction. The location of the arginines indicates formation of negative charges during the reaction at the transferred phosphoryl group, but not at the phosphate bridging oxygen atoms. This is consistent with an associative phosphoryl transfer mechanism but not with a dissociative one.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20353400 J.L.Whittingham, J.Carrero-Lerida, J.A.Brannigan, L.M.Ruiz-Perez, A.P.Silva, M.J.Fogg, A.J.Wilkinson, I.H.Gilbert, K.S.Wilson, and D.González-Pacanowska (2010).
Structural basis for the efficient phosphorylation of AZT-MP (3'-azido-3'-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase.
  Biochem J, 428, 499-509.
PDB codes: 2wwf 2wwg 2wwh 2wwi
18463139 C.Gondeau, L.Chaloin, P.Lallemand, B.Roy, C.Périgaud, T.Barman, A.Varga, M.Vas, C.Lionne, and S.T.Arold (2008).
Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase.
  Nucleic Acids Res, 36, 3620-3629.
PDB codes: 2zgv 3c39 3c3a 3c3b 3c3c
18662000 M.De Vivo, M.Dal Peraro, and M.L.Klein (2008).
Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.
  J Am Chem Soc, 130, 10955-10962.  
17154432 A.K.Hirsch, F.R.Fischer, and F.Diederich (2007).
Phosphate recognition in structural biology.
  Angew Chem Int Ed Engl, 46, 338-352.  
17212419 M.De Vivo, B.Ensing, M.Dal Peraro, G.A.Gomez, D.W.Christianson, and M.L.Klein (2007).
Proton shuttles and phosphatase activity in soluble epoxide hydrolase.
  J Am Chem Soc, 129, 387-394.  
  17183161 M.V.Dias, L.M.Faím, I.B.Vasconcelos, J.S.de Oliveira, L.A.Basso, D.S.Santos, and W.F.de Azevedo (2007).
Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1-6.
PDB codes: 2dfn 2dft
16672241 M.Bellinzoni, A.Haouz, M.Graña, H.Munier-Lehmann, W.Shepard, and P.M.Alzari (2006).
The crystal structure of Mycobacterium tuberculosis adenylate kinase in complex with two molecules of ADP and Mg2+ supports an associative mechanism for phosphoryl transfer.
  Protein Sci, 15, 1489-1493.
PDB code: 2cdn
15647264 A.Gorrell, S.H.Lawrence, and J.G.Ferry (2005).
Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila.
  J Biol Chem, 280, 10731-10742.
PDB codes: 1tuu 1tuy
15163660 D.Segura-Peña, N.Sekulic, S.Ort, M.Konrad, and A.Lavie (2004).
Substrate-induced conformational changes in human UMP/CMP kinase.
  J Biol Chem, 279, 33882-33889.
PDB code: 1tev
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
15229653 R.Kagawa, M.G.Montgomery, K.Braig, A.G.Leslie, and J.E.Walker (2004).
The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride.
  EMBO J, 23, 2734-2744.
PDB codes: 1w0j 1w0k 1w0q
15150266 Z.Ahmad, and A.E.Senior (2004).
Mutagenesis of residue betaArg-246 in the phosphate-binding subdomain of catalytic sites of Escherichia coli F1-ATPase.
  J Biol Chem, 279, 31505-31513.  
12694191 C.Pasti, S.Gallois-Montbrun, H.Munier-Lehmann, M.Veron, A.M.Gilles, and D.Deville-Bonne (2003).
Reaction of human UMP-CMP kinase with natural and analog substrates.
  Eur J Biochem, 270, 1784-1790.  
14573872 L.Yu, J.Mack, P.J.Hajduk, S.J.Kakavas, A.Y.Saiki, C.G.Lerner, and E.T.Olejniczak (2003).
Solution structure and function of an essential CMP kinase of Streptococcus pneumoniae.
  Protein Sci, 12, 2613-2621.
PDB code: 1q3t
12044161 A.Cook, E.D.Lowe, E.D.Chrysina, V.T.Skamnaki, N.G.Oikonomakos, and L.N.Johnson (2002).
Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism.
  Biochemistry, 41, 7301-7311.
PDB code: 1gy3
12324998 M.C.Hutter, and V.Helms (2002).
The mechanism of phosphorylation of natural nucleosides and anti-HIV analogues by nucleoside diphosphate kinase is independent of their sugar substituents.
  Chembiochem, 3, 643-651.  
11896404 Madhusudan, P.Akamine, N.H.Xuong, and S.S.Taylor (2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
  Nat Struct Biol, 9, 273-277.
PDB code: 1l3r
12036965 N.Sekulic, L.Shuvalova, O.Spangenberg, M.Konrad, and A.Lavie (2002).
Structural characterization of the closed conformation of mouse guanylate kinase.
  J Biol Chem, 277, 30236-30243.
PDB code: 1lvg
11863460 P.J.O'Brien, and D.Herschlag (2002).
Alkaline phosphatase revisited: hydrolysis of alkyl phosphates.
  Biochemistry, 41, 3207-3225.  
11960978 R.D.Miles, A.Gorrell, and J.G.Ferry (2002).
Evidence for a transition state analog, MgADP-aluminum fluoride-acetate, in acetate kinase from Methanosarcina thermophila.
  J Biol Chem, 277, 22547-22552.  
11112536 B.Schneider, C.Sigalat, T.Amano, and J.L.Zimmermann (2000).
Evidence for changes in the nucleotide conformation in the active site of H(+)-ATPase as determined by pulsed EPR spectroscopy.
  Biochemistry, 39, 15500-15512.  
11123913 I.M.Li de La Sierra, J.Gallay, M.Vincent, T.Bertrand, P.Briozzo, O.Bârzu, and A.M.Gilles (2000).
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling.
  Biochemistry, 39, 15870-15878.  
10873854 K.Braig, R.I.Menz, M.G.Montgomery, A.G.Leslie, and J.E.Walker (2000).
Structure of bovine mitochondrial F(1)-ATPase inhibited by Mg(2+) ADP and aluminium fluoride.
  Structure, 8, 567-573.
PDB codes: 1e1q 1e1r
10736166 K.Singh-Wissmann, R.D.Miles, C.Ingram-Smith, and J.G.Ferry (2000).
Identification of essential arginines in the acetate kinase from Methanosarcina thermophila.
  Biochemistry, 39, 3671-3677.  
  11152133 M.C.Hutter, and V.Helms (2000).
Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
  Protein Sci, 9, 2225-2231.  
10873853 N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, and A.Lavie (2000).
Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate.
  Structure, 8, 629-642.
PDB codes: 1e2d 1e2e 1e2f 1e2g 1e2q
10924155 S.Nadanaciva, J.Weber, and A.E.Senior (2000).
New probes of the F1-ATPase catalytic transition state reveal that two of the three catalytic sites can assume a transition state conformation simultaneously.
  Biochemistry, 39, 9583-9590.  
10555980 D.L.Graham, J.F.Eccleston, C.W.Chung, and P.N.Lowe (1999).
Magnesium fluoride-dependent binding of small G proteins to their GTPase-activating proteins.
  Biochemistry, 38, 14981-14987.  
10353838 P.Gonin, Y.Xu, L.Milon, S.Dabernat, M.Morr, R.Kumar, M.L.Lacombe, J.Janin, and I.Lascu (1999).
Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.
  Biochemistry, 38, 7265-7272.
PDB code: 1b99
10200157 S.J.Admiraal, B.Schneider, P.Meyer, J.Janin, M.Véron, D.Deville-Bonne, and D.Herschlag (1999).
Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase.
  Biochemistry, 38, 4701-4711.
PDB code: 1b4s
10066761 S.Nadanaciva, J.Weber, and A.E.Senior (1999).
Binding of the transition state analog MgADP-fluoroaluminate to F1-ATPase.
  J Biol Chem, 274, 7052-7058.  
9521686 A.Lavie, M.Konrad, R.Brundiers, R.S.Goody, I.Schlichting, and J.Reinstein (1998).
Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) at 2.0 A resolution: implications for catalysis and AZT activation.
  Biochemistry, 37, 3677-3686.
PDB code: 3tmk
9826650 A.Lavie, N.Ostermann, R.Brundiers, R.S.Goody, J.Reinstein, M.Konrad, and I.Schlichting (1998).
Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.
  Proc Natl Acad Sci U S A, 95, 14045-14050.
PDB codes: 4tmk 5tmp
9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
  9865950 H.Käck, J.Sandmark, K.J.Gibson, G.Schneider, and Y.Lindqvist (1998).
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
  Protein Sci, 7, 2560-2566.
PDB codes: 1bs1 1dam
9715904 M.B.Berry, and G.N.Phillips (1998).
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
9862805 P.Briozzo, B.Golinelli-Pimpaneau, A.M.Gilles, J.F.Gaucher, S.Burlacu-Miron, H.Sakamoto, J.Janin, and O.Bârzu (1998).
Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity.
  Structure, 6, 1517-1527.
PDB codes: 1cke 2cmk
9382787 A.Wittinghofer (1997).
Signaling mechanistics: aluminum fluoride for molecule of the year.
  Curr Biol, 7, R682-R685.  
9302992 M.R.Ahmadian, P.Stege, K.Scheffzek, and A.Wittinghofer (1997).
Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras.
  Nat Struct Biol, 4, 686-689.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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