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PDBsum entry 2rd5

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protein ligands metals Protein-protein interface(s) links
Protein binding PDB id
2rd5
Jmol
Contents
Protein chains
281 a.a. *
125 a.a. *
Ligands
ARG ×2
ADP ×2
NLG ×2
ATP ×2
Metals
_MG ×3
Waters ×64
* Residue conservation analysis
PDB id:
2rd5
Name: Protein binding
Title: Structural basis for the regulation of n-acetylglutamate kin in arabidopsis thaliana
Structure: Acetylglutamate kinase-like protein. Chain: a, b. Engineered: yes. Pii protein. Chain: c, d. Synonym: p ii nitrogen sensing protein glb i, at4g01900. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: t8h10.160. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: at4g01900, t7b11.16.
Resolution:
2.51Å     R-factor:   0.203     R-free:   0.229
Authors: Y.Mizuno,G.B.G.Moorhead,K.K.S.Ng
Key ref:
Y.Mizuno et al. (2007). Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana. J Biol Chem, 282, 35733-35740. PubMed id: 17913711 DOI: 10.1074/jbc.M707127200
Date:
21-Sep-07     Release date:   02-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9SCL7  (NAGK_ARATH) -  Acetylglutamate kinase, chloroplastic
Seq:
Struc:
347 a.a.
281 a.a.
Protein chains
Pfam   ArchSchema ?
Q9ZST4  (GLNB_ARATH) -  Nitrogen regulatory protein P-II homolog
Seq:
Struc:
196 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: 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
Bound ligand (Het Group name = ATP)
corresponds exactly
+
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     regulation of nitrogen utilization   3 terms 
  Biochemical function     enzyme regulator activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M707127200 J Biol Chem 282:35733-35740 (2007)
PubMed id: 17913711  
 
 
Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana.
Y.Mizuno, G.B.Moorhead, K.K.Ng.
 
  ABSTRACT  
 
PII is a highly conserved regulatory protein found in organisms across the three domains of life. In cyanobacteria and plants, PII relieves the feedback inhibition of the rate-limiting step in arginine biosynthesis catalyzed by N-acetylglutamate kinase (NAGK). To understand the molecular structural basis of enzyme regulation by PII, we have determined a 2.5-A resolution crystal structure of a complex formed between two homotrimers of PII and a single hexamer of NAGK from Arabidopsis thaliana bound to the metabolites N-acetylglutamate, ADP, ATP, and arginine. In PII, the T-loop and Trp(22) at the start of the alpha1-helix, which are both adjacent to the ATP-binding site of PII, contact two beta-strands as well as the ends of two central helices (alphaE and alphaG) in NAGK, the opposing ends of which form major portions of the ATP and N-acetylglutamate substrate-binding sites. The binding of Mg(2+).ATP to PII stabilizes a conformation of the T-loop that favors interactions with both open and closed conformations of NAGK. Interactions between PII and NAGK appear to limit the degree of opening and closing of the active-site cleft in opposition to a domain-separating inhibitory effect exerted by arginine, thus explaining the stimulatory effect of PII on the kinetics of arginine-inhibited NAGK.
 
  Selected figure(s)  
 
Figure 1.
Overall structure of the PII·NAGK complex.A and B, top and bottom views, respectively, along the molecular 3-fold rotational axis; C, side view along the 2-fold axis bisecting interface A; D, side view along the 2-fold axis bisecting interface B. In A and B, the views taken in C and D are marked with gray letters beside the respective 2-fold rotational axes. In C and D, the views taken in A and B are marked with gray letters beside the 3-fold rotational axis. PII is colored dark gray; ATP bound to PII and ADP bound to NAGK are colored magenta. NAGK protomers are colored yellow and green; N-acetylglutamate (NAG) is colored red, and arginine is colored blue. Figs. 1, 2, 3, 4 were prepared using PyMOL (38).
Figure 4.
Open and closed conformations of NAGK drawn as α-carbon traces. Shown are the open (A) and closed (B) conformations of A. thaliana NAGK and the open conformation of T. maritima NAGK bound to arginine (C) (21). ADP and N-acetylglutamate (NAG) are drawn in stick representation. The N-terminal domain (N-term; residues 15-211) is colored blue, and the C-terminal domain (C-term; residues 212-297) is colored red. The black dot marks the position of the rotational axis that is normal to the plane of the page. Rotating the N-terminal domain of the open form of NAGK by 11° about this axis in the direction indicated by the arrow in A would result in the closed conformation shown in B. The right panels show a “top” view similar to that used in Fig. 2A. This view is perpendicular to the rotational axis, which is drawn as a light gray arrow.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 35733-35740) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265771 M.Radchenko, and M.Merrick (2011).
The role of effector molecules in signal transduction by PII proteins.
  Biochem Soc Trans, 39, 189-194.  
20018655 A.B.Feria Bourrellier, B.Valot, A.Guillot, F.Ambard-Bretteville, J.Vidal, and M.Hodges (2010).
Chloroplast acetyl-CoA carboxylase activity is 2-oxoglutarate-regulated by interaction of PII with the biotin carboxyl carrier subunit.
  Proc Natl Acad Sci U S A, 107, 502-507.  
20716687 J.L.Llácer, J.Espinosa, M.A.Castells, A.Contreras, K.Forchhammer, and V.Rubio (2010).
Structural basis for the regulation of NtcA-dependent transcription by proteins PipX and PII.
  Proc Natl Acad Sci U S A, 107, 15397-15402.
PDB codes: 2xg8 2xgx 2xhk 2xko 2xkp
20521335 N.D.Shetty, M.C.Reddy, S.K.Palaninathan, J.L.Owen, and J.C.Sacchettini (2010).
Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein.
  Protein Sci, 19, 1513-1524.
PDB codes: 3bzq 3lf0
21041661 O.Fokina, V.R.Chellamuthu, K.Forchhammer, and K.Zeth (2010).
Mechanism of 2-oxoglutarate signaling by the Synechococcus elongatus PII signal transduction protein.
  Proc Natl Acad Sci U S A, 107, 19760-19765.
PDB codes: 2xul 2xzw
19131333 L.F.Huergo, M.Merrick, R.A.Monteiro, L.S.Chubatsu, M.B.Steffens, F.O.Pedrosa, and E.M.Souza (2009).
In vitro interactions between the PII proteins and the nitrogenase regulatory enzymes dinitrogenase reductase ADP-ribosyltransferase (DraT) and dinitrogenase reductase-activating glycohydrolase (DraG) in Azospirillum brasilense.
  J Biol Chem, 284, 6674-6682.  
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.  
  18453701 B.Bagautdinov, Y.Matsuura, S.Bagautdinova, N.Kunishima, and K.Yutani (2008).
Structure of putative CutA1 from Homo sapiens determined at 2.05 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 351-357.
PDB code: 2zfh
19013524 J.L.Llácer, I.Fita, and V.Rubio (2008).
Arginine and nitrogen storage.
  Curr Opin Struct Biol, 18, 673-681.  
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.