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PDBsum entry 1oha

Go to PDB code: 
protein ligands metals links
Kinase PDB id
1oha
Jmol
Contents
Protein chain
258 a.a. *
Ligands
ADP
NLG
ACT
Metals
_MG
Waters ×141
* Residue conservation analysis
PDB id:
1oha
Name: Kinase
Title: Acetylglutamate kinase from escherichia coli complexed with mgadp and n-acetyl-l-glutamate
Structure: Acetylglutamate kinase. Chain: a. Synonym: NAG kinase, agk, n-acetyl-l-glutamate 5-phosphotransferase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: bl21(de3). Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.9Å     R-factor:   0.200     R-free:   0.229
Authors: F.Gil-Ortiz,S.Ramon-Maiques,I.Fita,V.Rubio
Key ref:
F.Gil-Ortiz et al. (2003). The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic. J Mol Biol, 331, 231-244. PubMed id: 12875848 DOI: 10.1016/S0022-2836(03)00716-2
Date:
23-May-03     Release date:   31-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A6C8  (ARGB_ECOLI) -  Acetylglutamate kinase
Seq:
Struc:
258 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.2.8  - Acetylglutamate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Ornithine Biosynthesis
      Reaction: ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate
ATP
+
N-acetyl-L-glutamate
Bound ligand (Het Group name = NLG)
corresponds exactly
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ N-acetyl-L-glutamate 5-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(03)00716-2 J Mol Biol 331:231-244 (2003)
PubMed id: 12875848  
 
 
The course of phosphorus in the reaction of N-acetyl-L-glutamate kinase, determined from the structures of crystalline complexes, including a complex with an AlF(4)(-) transition state mimic.
F.Gil-Ortiz, S.Ramón-Maiques, I.Fita, V.Rubio.
 
  ABSTRACT  
 
N-Acetyl-L-glutamate kinase (NAGK), the structural paradigm of the enzymes of the amino acid kinase family, catalyzes the phosphorylation of the gamma-COO(-) group of N-acetyl-L-glutamate (NAG) by ATP. We determine here the crystal structures of NAGK complexes with MgADP, NAG and the transition-state analog AlF(4)(-); with MgADP and NAG; and with ADP and SO(4)(2-). Comparison of these structures with that of the MgAMPPNP-NAG complex allows to delineate three successive steps during phosphoryl transfer: at the beginning, when the attacking and leaving O atoms and the P atom are imperfectly aligned and the distance between the attacking O atom and the P atom is 2.8A; midway, at the bipyramidal intermediate, with nearly perfect alignment and a distance of 2.3A; and, when the transfer is completed. The transfer occurs in line and is strongly associative, with Lys8 and Lys217 stabilizing the transition state and the leaving group, respectively, and with Lys61, in contrast with an earlier proposal, not being involved. Three water molecules found in all the complexes play, together with Asp162 and the Mg, crucial structural roles. Two glycine-rich loops (beta1-alphaA and beta2-alphaB) are also very important, moving in the different complexes in concert with the ligands, to which they are hydrogen-bonded, either locking them in place for reaction or stabilizing the transition state. The active site is too narrow to accommodate the substrates without compressing the reacting groups, and this compressive strain appears a crucial component of the catalytic mechanism of NAGK, and possibly of other enzymes of the amino acid kinase family such as carbamate kinase. Initial binding of the two substrates would require a different enzyme conformation with a wider active site, and the energy of substrate binding would be used to change the conformation of the active center, causing substrate strain towards the transition state.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. 2F[obs] -F[calc] maps containing ball-and-stick models of the groups involved in phosphoryl group transfer in the complexes with MgADP-AlF[4]^ --NAG (a), MgAMPPNP-NAG (b) and MgADP-NAG (c). In the MgADP-NAG complex two water molecules occupying an intermediate position between ADP and NAG are also represented as cyan spheres. The indicated interatomic distances and angles are given.
Figure 5.
Figure 5. Stereoview ball-and-stick representation of the phosphoryl group transfer site in the NAGK complexes with MgAMPPNP-NAG (a), MgADP-AlF[4]^ --NAG (b), MgADP-NAG (c) and ADP-SO[4]^2 - (d). Of the ligands only the polyphosphate chain of the nucleotide and the g-carboxylate group of NAG are represented. Mg ion and water molecules are drawn as purple and cyan spheres, respectively. Nearby protein residues are shown in thinner trace. Hydrogen bonds and coordination bonds with Mg are shown as red broken lines, indicating the interatomic distances in Å. In (a) the interatomic distance between the attacking O atom of NAG and the g-P atom is represented with a blue broken line. AlF[4]^ - is shown in green.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 231-244) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20386738 E.Marcos, R.Crehuet, and I.Bahar (2010).
On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm.
  PLoS Comput Biol, 6, e1000738.  
  20392112 N.Dellas, and J.P.Noel (2010).
Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates.
  ACS Chem Biol, 5, 589-601.
PDB codes: 3k4o 3k4y 3k52 3k56
18446244 E.Marcos, J.M.Anglada, and R.Crehuet (2008).
Description of pentacoordinated phosphorus under an external electric field: which basis sets and semi-empirical methods are needed?
  Phys Chem Chem Phys, 10, 2442-2450.  
19013524 J.L.Llácer, I.Fita, and V.Rubio (2008).
Arginine and nitrogen storage.
  Curr Opin Struct Biol, 18, 673-681.  
18263723 M.L.Fernández-Murga, and V.Rubio (2008).
Basis of arginine sensitivity of microbial N-acetyl-L-glutamate kinases: mutagenesis and protein engineering study with the Pseudomonas aeruginosa and Escherichia coli enzymes.
  J Bacteriol, 190, 3018-3025.  
18701452 S.Pakhomova, S.G.Bartlett, A.Augustus, T.Kuzuyama, and M.E.Newcomer (2008).
Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.
  J Biol Chem, 283, 28518-28526.
PDB codes: 3d40 3d41
17488874 A.T.Torelli, J.Krucinska, and J.E.Wedekind (2007).
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
  RNA, 13, 1052-1070.
PDB codes: 2p7d 2p7e 2p7f
17913711 Y.Mizuno, G.B.Moorhead, and K.K.Ng (2007).
Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana.
  J Biol Chem, 282, 35733-35740.
PDB code: 2rd5
16411744 J.Salter, J.Krucinska, S.Alam, V.Grum-Tokars, and J.E.Wedekind (2006).
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.
  Biochemistry, 45, 686-700.
PDB codes: 1zfr 1zft 1zfv 1zfx 2bcy 2bcz 2fgp 2oue
16905770 M.Kotaka, J.Ren, M.Lockyer, A.R.Hawkins, and D.K.Stammers (2006).
Structures of R- and T-state Escherichia coli aspartokinase III. Mechanisms of the allosteric transition and inhibition by lysine.
  J Biol Chem, 281, 31544-31552.
PDB codes: 2j0w 2j0x
15857829 P.Briozzo, C.Evrin, P.Meyer, L.Assairi, N.Joly, O.Barzu, and A.M.Gilles (2005).
Structure of Escherichia coli UMP kinase differs from that of other nucleoside monophosphate kinases and sheds new light on enzyme regulation.
  J Biol Chem, 280, 25533-25540.
PDB codes: 2bnd 2bne 2bnf
15342584 M.L.Fernández-Murga, F.Gil-Ortiz, J.L.Llácer, and V.Rubio (2004).
Arginine biosynthesis in Thermotoga maritima: characterization of the arginine-sensitive N-acetyl-L-glutamate kinase.
  J Bacteriol, 186, 6142-6149.  
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.