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PDBsum entry 1del

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protein ligands metals Protein-protein interface(s) links
Phosphotransferase PDB id
1del
Jmol
Contents
Protein chains
241 a.a. *
Ligands
DGP ×2
AMP
Metals
_MG ×2
Waters ×222
* Residue conservation analysis
PDB id:
1del
Name: Phosphotransferase
Title: Deoxynucleoside monophosphate kinase complexed with deoxy-gm
Structure: Deoxynucleoside monophosphate kinase. Chain: a, b. Engineered: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665. Gene: 1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.186    
Authors: A.Teplyakov,P.Sebastiao
Key ref: A.Teplyakov et al. (1996). Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP. EMBO J, 15, 3487-3497. PubMed id: 8670851
Date:
09-Jan-96     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04531  (DNMK_BPT4) -  Deoxynucleotide monophosphate kinase
Seq:
Struc:
241 a.a.
241 a.a.
Key:    PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.13  - (Deoxy)nucleoside-phosphate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + deoxynucleoside phosphate = ADP + deoxynucleoside diphosphate
ATP
+
deoxynucleoside phosphate
Bound ligand (Het Group name = DGP)
matches with 50.00% similarity
=
ADP
Bound ligand (Het Group name = AMP)
matches with 85.19% similarity
+ deoxynucleoside diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   1 term 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
EMBO J 15:3487-3497 (1996)
PubMed id: 8670851  
 
 
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, K.S.Wilson.
 
  ABSTRACT  
 
NMP kinases catalyse the phosphorylation of the canonical nucleotides to the corresponding diphosphates using ATP as a phosphate donor. Bacteriophage T4 deoxynucleotide kinase (DNK) is the only member of this family of enzymes that recognizes three structurally dissimilar nucleotides: dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The crystal structure of DNK with its substrate dGMP has been determined at 2.0 A resolution by single isomorphous replacement. The structure of the ternary complex with dGMP and ATP has been determined at 2.2 A resolution. The polypeptide chain of DNK is folded into two domains of equal size, one of which resembles the mononucleotide binding motif with the glycine-rich P-loop. The second domain, consisting of five alpha-helices, forms the NMP binding pocket. A hinge connection between the domains allows for large movements upon substrate binding which are not restricted by dimerization of the enzyme. The mechanism of active centre formation via domain closure is described. Comparison with other P-loop-containing proteins indicates an induced-fit mode of NTP binding. Protein-substrate interactions observed at the NMP and NTP sites provide the basis for understanding the principles of nucleotide discrimination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18798562 A.L.Olson, H.Yao, T.J.Herdendorf, H.M.Miziorko, S.Hannongbua, P.Saparpakorn, S.Cai, and D.S.Sem (2009).
Substrate induced structural and dynamics changes in human phosphomevalonate kinase and implications for mechanism.
  Proteins, 75, 127-138.  
18618710 Q.Chang, X.X.Yan, S.Y.Gu, J.F.Liu, and D.C.Liang (2008).
Crystal structure of human phosphomevalonate kinase at 1.8 A resolution.
  Proteins, 73, 254-258.
PDB code: 3ch4
18247412 Y.Meroz, and D.Horn (2008).
Biological roles of specific peptides in enzymes.
  Proteins, 72, 606-612.  
17902708 T.J.Herdendorf, and H.M.Miziorko (2007).
Functional evaluation of conserved basic residues in human phosphomevalonate kinase.
  Biochemistry, 46, 11780-11788.  
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
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
  9336833 K.Wild, T.Bohner, G.Folkers, and G.E.Schulz (1997).
The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.
  Protein Sci, 6, 2097-2106.
PDB codes: 1vtk 2vtk 3vtk
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.