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PDBsum entry 1e2f
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protein ligands metals links
Transferase PDB id
1e2f

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
210 a.a. *
Ligands
TMP
ANP
ADP
Metals
_MG ×2
Waters ×297
* Residue conservation analysis
PDB id:
1e2f
Name: Transferase
Title: Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate and a magnesium-ion
Structure: Thymidylate kinase. Chain: a. Synonym: tmpk. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.60Å     R-factor:   0.210     R-free:   0.264
Authors: N.Ostermann,I.Schlichting,R.Brundiers,M.Konrad,J.Reinstein,T.Veit, R.S.Goody,A.Lavie
Key ref:
N.Ostermann et al. (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. PubMed id: 10873853 DOI: 10.1016/S0969-2126(00)00149-0
Date:
22-May-00     Release date:   17-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P23919  (KTHY_HUMAN) -  Thymidylate kinase from Homo sapiens
Seq:
Struc: 		212 a.a.
210 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.9  - dTMP kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dTMP + ATP = dTDP + ADP
dTMP
 +
ATP
Bound ligand (Het Group name = TMP)
corresponds exactly 		=
dTDP
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ ADP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00149-0 Structure 8:629-642 (2000)
PubMed id: 10873853  
 
 
Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate.
N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, A.Lavie.
 
  ABSTRACT  
 
BACKGROUND: Thymidylate kinase (TMPK) is a nucleoside monophosphate kinase that catalyzes the reversible phosphoryltransfer between ATP and TMP to yield ADP and TDP. In addition to its vital role in supplying precursors for DNA synthesis, human TMPK has an important medical role participating in the activation of a number of anti-HIV prodrugs. RESULTS: Crystal structures of human TMPK in complex with TMP and ADP, TMP and the ATP analog AppNHp, TMP with ADP and the phosphoryl analog AlF(3), TDP and ADP, and the bisubstrate analog TP(5)A were determined. The conformations of the P-loop, the LID region, and the adenine-binding loop vary according to the nature of the complex. Substitution of ADP by AppNHp results in partial closure of the P-loop and the rotation of the TMP phosphate group to a catalytically unfavorable position, which rotates back in the AlF(3) complex to a position suitable for in-line attack. In the fully closed state observed in the TP(5)A and the TDP-ADP complexes, Asp15 interacts strongly with the 3'-hydroxyl group of TMP. CONCLUSIONS: The observed changes of nucleotide state and conformation and the corresponding protein structural changes are correlated with intermediates occurring along the reaction coordinate and show the sequence of events occurring during phosphate transfer. The low catalytic activity of human TMPK appears to be determined by structural changes required to achieve catalytic competence and it is suggested that a mechanism might exist to accelerate the activity.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Conformational changes of Arg97 and the phosphoryl groups of TDP to the stable product conformation in the TDP-ADP bound complex. Overlay of the TMP/TDP-binding site of the structures of TMPK in complex with TMP, ADP and AlF[3] (red) and TDP and ADP (yellow). In the complex with bound TDP and ADP the sidechain of Arg97 rotates (90°) around the bond between the atoms CG and CD such that it cannot act as a clamp to bring both nucleotides together for the backward reaction. The figures were generated using the programs Molscript [28] and Raster 3D [29].
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 629-642) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20007608 H.M.Chu, T.P.Ko, and A.H.Wang (2010).
Crystal structure and substrate specificity of plant adenylate isopentenyltransferase from Humulus lupulus: distinctive binding affinity for purine and pyrimidine nucleotides.
  Nucleic Acids Res, 38, 1738-1748.
PDB code: 3a8t
20065942 J.J.Kohler, S.H.Hosseini, I.Cucoranu, O.Zhelyabovska, E.Green, K.Ivey, A.Abuin, E.Fields, A.Hoying, R.Russ, R.Santoianni, C.M.Raper, Q.Yang, A.Lavie, and W.Lewis (2010).
Transgenic cardiac-targeted overexpression of human thymidylate kinase.
  Lab Invest, 90, 383-390.  
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
19029291 Y.W.Tan, J.A.Hanson, and H.Yang (2009).
Direct Mg2+ Binding Activates Adenylate Kinase from Escherichia coli.
  J Biol Chem, 284, 3306-3313.  
18559937 A.Lavie, Y.Su, M.Ghassemi, R.M.Novak, M.Caffrey, N.Sekulic, C.Monnerjahn, M.Konrad, and J.L.Cook (2008).
Restoration of the antiviral activity of 3'-azido-3'-deoxythymidine (AZT) against AZT-resistant human immunodeficiency virus by delivery of engineered thymidylate kinase to T cells.
  J Gen Virol, 89, 1672-1679.  
18523102 C.Carnrot, L.Wang, D.Topalis, and S.Eriksson (2008).
Mechanisms of substrate selectivity for Bacillus anthracis thymidylate kinase.
  Protein Sci, 17, 1486-1493.  
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
18384378 N.E.Mikkelsen, B.Munch-Petersen, and H.Eklund (2008).
Structural studies of nucleoside analog and feedback inhibitor binding to Drosophila melanogaster multisubstrate deoxyribonucleoside kinase.
  FEBS J, 275, 2151-2160.
PDB codes: 2jj8 2vp0 2vp2 2vp4 2vp5 2vp6 2vp9 2vqs
17459874 L.Miallau, W.N.Hunter, S.M.McSweeney, and G.A.Leonard (2007).
Structures of Staphylococcus aureus D-tagatose-6-phosphate kinase implicate domain motions in specificity and mechanism.
  J Biol Chem, 282, 19948-19957.
PDB codes: 2jg1 2jgv
17902708 T.J.Herdendorf, and H.M.Miziorko (2007).
Functional evaluation of conserved basic residues in human phosphomevalonate kinase.
  Biochemistry, 46, 11780-11788.  
16288457 G.Hible, P.Christova, L.Renault, E.Seclaman, A.Thompson, E.Girard, H.Munier-Lehmann, and J.Cherfils (2006).
Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase.
  Proteins, 62, 489-500.
PDB codes: 1znw 1znx 1zny 1znz
16336263 D.Topalis, B.Collinet, C.Gasse, L.Dugué, J.Balzarini, S.Pochet, and D.Deville-Bonne (2005).
Substrate specificity of vaccinia virus thymidylate kinase.
  FEBS J, 272, 6254-6265.  
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
15208312 O.Barabás, V.Pongrácz, J.Kovári, M.Wilmanns, and B.G.Vértessy (2004).
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
  J Biol Chem, 279, 42907-42915.
PDB codes: 1rn8 1rnj 1seh 1syl
12454011 A.Haouz, V.Vanheusden, H.Munier-Lehmann, M.Froeyen, P.Herdewijn, S.Van Calenbergh, and M.Delarue (2003).
Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism.
  J Biol Chem, 278, 4963-4971.
PDB codes: 1mrn 1mrs
12616626 C.Monnerjahn, and M.Konrad (2003).
Modulated nucleoside kinases as tools to improve the activation of therapeutic nucleoside analogues.
  Chembiochem, 4, 143-146.  
12808445 E.Sabini, S.Ort, C.Monnerjahn, M.Konrad, and A.Lavie (2003).
Structure of human dCK suggests strategies to improve anticancer and antiviral therapy.
  Nat Struct Biol, 10, 513-519.
PDB codes: 1p5z 1p60 1p61 1p62
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
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 code is shown on the right.

 

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