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PDBsum entry 2bty

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2bty
Jmol
Contents
Protein chains
282 a.a. *
Ligands
ARG ×3
NLG ×3
Metals
__K
Waters ×46
* Residue conservation analysis
PDB id:
2bty
Name: Transferase
Title: Acetylglutamate kinase from thermotoga maritima complexed with its inhibitor arginine
Structure: Acetylglutamate kinase. Chain: a, b, c. Synonym: NAG kinase, agk, n-acetyl-l-glutamate 5-phosphotransferase. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.75Å     R-factor:   0.242     R-free:   0.273
Authors: F.Gil-Ortiz,M.L.Fernandez-Murga,I.Fita,V.Rubio
Key ref:
S.Ramón-Maiques et al. (2006). Structural Bases of Feed-back Control of Arginine Biosynthesis, Revealed by the Structures of Two Hexameric N-Acetylglutamate Kinases, from Thermotoga maritima and Pseudomonas aeruginosa. J Mol Biol, 356, 695-713. PubMed id: 16376937 DOI: 10.1016/j.jmb.2005.11.079
Date:
08-Jun-05     Release date:   13-Dec-05    
Supersedes: 1uvv
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X2A4  (ARGB_THEMA) -  Acetylglutamate kinase
Seq:
Struc:
282 a.a.
282 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
+ 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     metabolic process   5 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.11.079 J Mol Biol 356:695-713 (2006)
PubMed id: 16376937  
 
 
Structural Bases of Feed-back Control of Arginine Biosynthesis, Revealed by the Structures of Two Hexameric N-Acetylglutamate Kinases, from Thermotoga maritima and Pseudomonas aeruginosa.
S.Ramón-Maiques, M.L.Fernández-Murga, F.Gil-Ortiz, A.Vagin, I.Fita, V.Rubio.
 
  ABSTRACT  
 
N-Acetylglutamate kinase (NAGK) catalyses the second step in the route of arginine biosynthesis. In many organisms this enzyme is inhibited by the final product of the route, arginine, and thus plays a central regulatory role. In addition, in photosynthetic organisms NAGK is the target of the nitrogen-signalling protein P(II). The 3-D structure of homodimeric, arginine-insensitive, Escherichia coli NAGK, clarified substrate binding and catalysis but shed no light on arginine inhibition of NAGK. We now shed light on arginine inhibition by determining the crystal structures, at 2.75A and 2.95A resolution, of arginine-complexed Thermotoga maritima and arginine-free Pseudomonas aeruginosa NAGKs, respectively. Both enzymes are highly similar ring-like hexamers having a central orifice of approximately 30A diameter. They are formed by linking three E.coli NAGK-like homodimers through the interlacing of an N-terminal mobile kinked alpha-helix, which is absent from E.coli NAGK. Arginine is bound in each subunit of T.maritima NAGK, flanking the interdimeric junction, in a site formed between the N helix and the C lobe of the subunit. This site is also present, in variable conformations, in P.aeruginosa NAGK, but is missing from E.coli NAGK. Arginine, by gluing the C lobe of each subunit to the inter-dimeric junction, may stabilize an enlarged active centre conformation, hampering catalysis. Acetylglutamate counters arginine inhibition by promoting active centre closure. The hexameric architecture justifies the observed sigmoidal arginine inhibition kinetics with a high Hill coefficient (N approximately 4), and appears essential for arginine inhibition and for NAGK-P(II) complex formation, since this complex may involve binding of NAGK and P(II) with their 3-fold axes aligned. The NAGK structures allow identification of diagnostic sequence signatures for arginine inhibition. These signatures are found also in the homologous arginine-inhibited enzyme NAG synthase. The findings on NAGK shed light on the structure, function and arginine inhibition of this synthase, for which a hexameric model is constructed.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Architecture of arginine-sensitive NAGK. The TmNAGK ((a) and (b)) or PaNAGK ((e) and (f)) hexamers are viewed ((a) and (e)) along or ((b) and (f)) perpendicularly to the molecular 3-fold axis. Each homodimer is coloured differently. In (a) and (b) arginine, and in (e) and (f) MgADP and NAG are represented in space-filling representation and coloured. In (a) and (e) the arrowpoints indicate the interlaced N helices at one junction. (c) TmNAGK and (d) EcNAGK26 homodimers, viewed along their 2-fold axes. The N and C lobes are in blue and green, respectively, and the N helix is in red. In (c) arginine is shown in space-filling representation, and coloured. The ligands shown in (d) are in ball and stick representation, and are NAG and AMPPNP.
Figure 3.
Figure 3. Amino acid sequence and topology of secondary structure elements, and signature sequences of arginine-sensitive NAGK. (a) Sequence alignment of E. coli, P. aeruginosa and T. maritima NAGKs (Swissprot P0A6C8, Q9HTN2 and Q9X2A4, respectively), localizing the secondary structure elements as superimposed blue arrows (b-strands), and yellow (a-helices) or orange (N-terminal helix) rectangles. The residues conserved or conservatively replaced in all NAGKs are in red, those having decreased accessibility upon the binding of NAG, MgADP or arginine are indicated with dark green triangles, light green triangles and violet diamonds, respectively. Black and grey circles denote decreased accessibility upon homodimer and hexamer formation, respectively. Signature sequence traits associated with arginine inhibition are underlined. (b) Scheme of the topology of secondary structure elements found in NAGKs, where b-strands and a-helices are represented as triangles and circles, respectively, the strands of the central b-sheet are shadowed, and the colour code is red for the N helix (the only element missing in EcNAGK; represented as two circles because of the kink), and green and blue for the elements of the N and the C lobe, respectively. (c) Alignment (see Materials and Methods) of arginine-insensitive and arginine-sensitive NAGKs in the three regions (separated by vertical lines) where diagnostic signatures were identified. Residues found constantly and exclusively in arginine-sensitive NAGKs are highlighted in red. The K/R highlighted in blue is found constantly but not exclusively, in arginine-sensitive NAGKs. The residues highlighted in pink are exclusively (but not constantly) found in arginine-sensitive NAGKs. Yellow colouring highlights residues that are conserved or conservatively replaced in most NAGKs, irrespective of whether they are sensitive or insensitive to arginine. Rectangles and arrows above the alignment indicate, respectively, a-helices and b-strands, as they appear in PaNAGK. The horizontal line below the alignment marks the larger (see the text) sequence signature at the b15-aH-b16 region. A rectangle encloses the phenylalanine residues of yeast and Neurospora crassa NAGKs that when mutated resulted in hampered arginine inhibition.16 The abbreviations used and the Swissprot/Trembl (unless indicated otherwise) accession numbers (given between parentheses) are the following: ECOLI, E. coli (P0A6C8); SERMA, S. marcescens (encoded by nucleotides 4275578-4274805 of the S. marcescens genome, systematic_id=SMA4004, http://www.sanger.ac.uk/projects/s_marcescens/sma.art); BACSU, B. subtilis (P68729); BACST, Bacillus stearothermophilus (Q07905); PSEAE, P. aeruginosa (Q9HTN2); THEMA, T. maritima (Q9X2A4); CORGL, Corynebacterium glutamicum;13 SYNP7, S. elongatus, strain PCC7942 (Q6V1L5). The sequences of photosynthetic eukaryotes start after a predicted chloroplast signal targeting sequence that precedes the N-terminal extension: CREIN, Chlamydomonas reinhardtii (gene TC25068, http://www.tigr.org/tdb/tgi/chrgi); ORYSA, Oriza sativa (rice, Q949B4); ARATH: Arabidopsis thaliana (Q8LA25); the rice and A. thaliana NAGKs are assumed to be arginine-sensitive by similarity to the pea enzyme18 (for which no sequence is available) and also because both are known to interact with the nitrogen signalling protein P[II].19^ and 21 The fungal sequences start after the mitochondrial signal targeting sequence that precedes the N-terminal extension: YEAST, Saccharomyces cerevisiae (Q01217); NEUCR, N. crassa (P54898).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 695-713) copyright 2006.  
  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.  
20544237 I.Pérez-Arellano, and J.Cervera (2010).
Glutamate kinase from Thermotoga maritima: characterization of a thermophilic enzyme for proline biosynthesis.
  Extremophiles, 14, 409-415.  
20303810 L.Caldovic, N.Ah Mew, D.Shi, H.Morizono, M.Yudkoff, and M.Tuchman (2010).
N-acetylglutamate synthase: structure, function and defects.
  Mol Genet Metab, 100, S13-S19.  
  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
19095660 L.Min, Z.Jin, L.Caldovic, H.Morizono, N.M.Allewell, M.Tuchman, and D.Shi (2009).
Mechanism of Allosteric Inhibition of N-Acetyl-L-glutamate Synthase by L-Arginine.
  J Biol Chem, 284, 4873-4880.
PDB codes: 3d2m 3d2p
19357433 M.S.Kalamaki, D.Alexandrou, D.Lazari, G.Merkouropoulos, V.Fotopoulos, I.Pateraki, A.Aggelis, A.Carrillo-López, M.J.Rubio-Cabetas, and A.K.Kanellis (2009).
Over-expression of a tomato N-acetyl-L-glutamate synthase gene (SlNAGS1) in Arabidopsis thaliana results in high ornithine levels and increased tolerance in salt and drought stresses.
  J Exp Bot, 60, 1859-1871.  
18184660 D.Shi, V.Sagar, Z.Jin, X.Yu, L.Caldovic, H.Morizono, N.M.Allewell, and M.Tuchman (2008).
The crystal structure of N-acetyl-L-glutamate synthase from Neisseria gonorrhoeae provides insights into mechanisms of catalysis and regulation.
  J Biol Chem, 283, 7176-7184.
PDB codes: 2r8v 2r98 3b8g
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.  
18801197 N.Haskins, M.Panglao, Q.Qu, H.Majumdar, J.Cabrera-Luque, H.Morizono, M.Tuchman, and L.Caldovic (2008).
Inversion of allosteric effect of arginine on N-acetylglutamate synthase, a molecular marker for evolution of tetrapods.
  BMC Biochem, 9, 24.  
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
17959776 J.L.Llácer, A.Contreras, K.Forchhammer, C.Marco-Marín, F.Gil-Ortiz, R.Maldonado, I.Fita, and V.Rubio (2007).
The crystal structure of the complex of PII and acetylglutamate kinase reveals how PII controls the storage of nitrogen as arginine.
  Proc Natl Acad Sci U S A, 104, 17644-17649.
PDB codes: 2jj4 2v5h
17425781 Q.Qu, H.Morizono, D.Shi, M.Tuchman, and L.Caldovic (2007).
A novel bifunctional N-acetylglutamate synthase-kinase from Xanthomonas campestris that is closely related to mammalian N-acetylglutamate synthase.
  BMC Biochem, 8, 4.  
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
17347518 Y.Xu, B.Labedan, and N.Glansdorff (2007).
Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms.
  Microbiol Mol Biol Rev, 71, 36-47.  
  17142901 D.Shi, L.Caldovic, Z.Jin, X.Yu, Q.Qu, L.Roth, H.Morizono, Y.Hathout, N.M.Allewell, and M.Tuchman (2006).
Expression, crystallization and preliminary crystallographic studies of a novel bifunctional N-acetylglutamate synthase/kinase from Xanthomonas campestris homologous to vertebrate N-acetylglutamate synthase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1218-1222.  
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.