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99 a.a.
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101 a.a.
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92 a.a.
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99 a.a.
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84 a.a.
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* Residue conservation analysis
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PDB id:
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Signaling protein
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Title:
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Structure of pii protein from herbaspirillum seropedicae
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Structure:
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Pii protein. Chain: a, b, c, d, e, f. Engineered: yes
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Source:
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Herbaspirillum seropedicae. Organism_taxid: 964. Gene: glnb. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Trimer (from
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Resolution:
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2.10Å
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R-factor:
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0.203
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R-free:
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0.272
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Authors:
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E.M.Benelli,M.Buck,I.Polikarpov,E.M.De Souza,L.M.Cruz,F.O.Pedrosa
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Key ref:
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E.Machado Benelli
et al.
(2002).
Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK.
Eur J Biochem,
269,
3296-3303.
PubMed id:
DOI:
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Date:
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10-Jan-01
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Release date:
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17-Jun-03
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PROCHECK
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Headers
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References
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P94852
(P94852_HERSE) -
Nitrogen regulatory P-II protein from Herbaspirillum seropedicae
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Seq:
Struc:
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112 a.a.
99 a.a.
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P94852
(P94852_HERSE) -
Nitrogen regulatory P-II protein from Herbaspirillum seropedicae
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Seq:
Struc:
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112 a.a.
101 a.a.
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P94852
(P94852_HERSE) -
Nitrogen regulatory P-II protein from Herbaspirillum seropedicae
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Seq:
Struc:
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112 a.a.
92 a.a.
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DOI no:
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Eur J Biochem
269:3296-3303
(2002)
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PubMed id:
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Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK.
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E.Machado Benelli,
M.Buck,
I.Polikarpov,
E.Maltempi de Souza,
L.M.Cruz,
F.O.Pedrosa.
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ABSTRACT
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PII-like proteins are signal transduction proteins found in bacteria, archaea
and eukaryotes. They mediate a variety of cellular responses. A second PII-like
protein, called GlnK, has been found in several organisms. In the diazotroph
Herbaspirillum seropedicae, PII protein is involved in sensing nitrogen levels
and controlling nitrogen fixation genes. In this work, the crystal structure of
the unliganded H. seropedicae PII was solved by X-ray diffraction. H.
seropedicae PII has a Gly residue, Gly108 preceding Pro109 and the main-chain
forms a beta turn. The glycine at position 108 allows a bend in the C-terminal
main-chain, thereby modifying the surface of the cleft between monomers and
potentially changing function. The structure suggests that the C-terminal region
of PII proteins may be involved in specificity of function, and nonenteric
diazotrophs are found to have the C-terminal consensus XGXDAX(107-112). We are
also proposing binding sites for ATP and 2-oxoglutarate based on the structural
alignment of PII with PII-ATP/GlnK-ATP, 5-carboxymethyl-2-hydroxymuconate
isomerase and 4-oxalocrotonate tautomerase bound to the inhibitor
2-oxo-3-pentynoate.
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Selected figure(s)
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Figure 1.
Fig. 1. Ribbon diagrams of the trimeric HsPII (A) and
monomeric HsPII, EcPII, EcPII-ATP, EcGlnK and EcGlnK-ATP (B).
(A) A ribbon diagram of the structure of the trimeric HsPII,
each chain in a different colour. The  sheets of the
 motif line
the central cavity of the trimer with the helices at the
periphery. (B) Ribbon diagrams of the monomers of HsPII (i),
EcPII (ii), EcPII-ATP (iii), EcGlnK (iv) and EcGlnK-ATP (v).
Secondary structures are colour coded: green sheets, 1–4, blue
helices, 1–2 and
3[10] helix and orange loops. The monomers share the same motif with
the major structural differences residing in the loops T and C.
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Figure 4.
Fig. 4. Model to ATP and 2-oxoglutarate binding sites in
HsPII protein. (A ) Diagram of a C trace overlay
of HsPII (orange) with CHMI (cyan) [31]. A top view of the
trimers similar in orientation to Figs 1A and 2Bii Go- . The
different views of the proposed 2-oxoglutarate and ATP-binding
sites in HsPII protein are shown in (B ), (C ) and (D). (B)
Position of ATP and 2-oxo-3-pentynoate in the lateral cleft of
HsPII. (C) ATP molecule and the neighbouring amino-acid
residues. (D ) 2-oxo-3-pentynoate molecule and the neighbour
amino-acid residues. Location of ATP and 2-oxo-3-pentynoate was
modelled using HsPII, EcGlnK-ATP, EcPII-ATP and 4-oxalocrotonate
tautomerase-2-oxo-3-pentynoate structures using dali and
lsqkab[8,14,15].
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
Eur J Biochem
(2002,
269,
3296-3303)
copyright 2002.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Bandyopadhyay,
A.Arora,
S.Jain,
A.Laskar,
C.Mandal,
V.A.Ivanisenko,
E.S.Fomin,
S.S.Pintus,
N.A.Kolchanov,
S.Maiti,
and
S.Ramachandran
(2010).
Expression and molecular characterization of the Mycobacterium tuberculosis PII protein.
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J Biochem,
147,
279-289.
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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.
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Protein Sci,
19,
1513-1524.
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PDB codes:
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F.Gruswitz,
J.O'Connell,
and
R.M.Stroud
(2007).
Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A.
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Proc Natl Acad Sci U S A,
104,
42-47.
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PDB code:
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M.J.Conroy,
A.Durand,
D.Lupo,
X.D.Li,
P.A.Bullough,
F.K.Winkler,
and
M.Merrick
(2007).
The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel.
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Proc Natl Acad Sci U S A,
104,
1213-1218.
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PDB code:
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O.Yildiz,
C.Kalthoff,
S.Raunser,
and
W.Kühlbrandt
(2007).
Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake.
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EMBO J,
26,
589-599.
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PDB codes:
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T.J.Lie,
and
J.A.Leigh
(2007).
Genetic screen for regulatory mutations in Methanococcus maripaludis and its use in identification of induction-deficient mutants of the euryarchaeal repressor NrpR.
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Appl Environ Microbiol,
73,
6595-6600.
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A.Durand,
and
M.Merrick
(2006).
In vitro analysis of the Escherichia coli AmtB-GlnK complex reveals a stoichiometric interaction and sensitivity to ATP and 2-oxoglutarate.
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J Biol Chem,
281,
29558-29567.
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A.Heinrich,
K.Woyda,
K.Brauburger,
G.Meiss,
C.Detsch,
J.Stülke,
and
K.Forchhammer
(2006).
Interaction of the membrane-bound GlnK-AmtB complex with the master regulator of nitrogen metabolism TnrA in Bacillus subtilis.
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J Biol Chem,
281,
34909-34917.
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Y.Zhang,
E.L.Pohlmann,
M.C.Conrad,
and
G.P.Roberts
(2006).
The poor growth of Rhodospirillum rubrum mutants lacking PII proteins is due to an excess of glutamine synthetase activity.
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Mol Microbiol,
61,
497-510.
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Y.Zhu,
M.C.Conrad,
Y.Zhang,
and
G.P.Roberts
(2006).
Identification of Rhodospirillum rubrum GlnB variants that are altered in their ability to interact with different targets in response to nitrogen status signals.
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J Bacteriol,
188,
1866-1874.
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K.Forchhammer
(2004).
Global carbon/nitrogen control by PII signal transduction in cyanobacteria: from signals to targets.
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FEMS Microbiol Rev,
28,
319-333.
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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.
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Links
