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PDBsum entry 1qgn
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* Residue conservation analysis
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PDB id:
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Lyase
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Title:
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Cystathionine gamma-synthase from nicotiana tabacum
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Structure:
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Protein (cystathionine gamma-synthase). Chain: a, b, c, d, e, f, g, h. Engineered: yes. Other_details: aldimine linkage between pyridoxal 5'-phosphate c4a and lys261 nz
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Source:
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Nicotiana tabacum. Common tobacco. Organism_taxid: 4097. Organelle: chloroplast. Gene: metb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Homo-Tetramer (from PDB file)
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Resolution:
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2.90Å
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R-factor:
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0.201
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R-free:
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0.250
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Authors:
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C.Steegborn,A.Messerschmidt,B.Laber,W.Streber,R.Huber,T.Clausen
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Key ref:
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C.Steegborn
et al.
(1999).
The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
J Mol Biol,
290,
983-996.
PubMed id:
DOI:
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Date:
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02-May-99
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Release date:
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25-Aug-99
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PROCHECK
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Headers
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References
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Q9ZPL5
(Q9ZPL5_TOBAC) -
Cystathionine gamma-synthase from Nicotiana tabacum
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Seq:
Struc:
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445 a.a.
398 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.4.2.99.9
- Transferred entry: 2.5.1.48.
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Reaction:
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O-succinyl-L-homoserine + L-cysteine = cystathionine + succinate
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DOI no:
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J Mol Biol
290:983-996
(1999)
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PubMed id:
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The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.
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C.Steegborn,
A.Messerschmidt,
B.Laber,
W.Streber,
R.Huber,
T.Clausen.
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ABSTRACT
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Cystathionine gamma-synthase catalyses the committed step of de novo methionine
biosynthesis in micro-organisms and plants, making the enzyme an attractive
target for the design of new antibiotics and herbicides. The crystal structure
of cystathionine gamma-synthase from Nicotiana tabacum has been solved by
Patterson search techniques using the structure of Escherichia coli
cystathionine gamma-synthase. The model was refined at 2.9 A resolution to a
crystallographic R -factor of 20.1 % (Rfree25.0 %). The physiological substrates
of the enzyme, L-homoserine phosphate and L-cysteine, were modelled into the
unliganded structure. These complexes support the proposed ping-pong mechanism
for catalysis and illustrate the dissimilar substrate specificities of bacterial
and plant cystathionine gamma-synthases on a molecular level. The main
difference arises from the binding modes of the distal substrate groups (O
-acetyl/succinyl versusO -phosphate). Central in fixing the distal phosphate of
the plant CGS substrate is an exposed lysine residue that is strictly conserved
in plant cystathionine gamma-synthases whereas bacterial enzymes carry a glycine
residue at this position. General insight regarding the reaction specificity of
transsulphuration enzymes is gained by the comparison to cystathionine
beta-lyase from E. coli, indicating the mechanistic importance of a second
substrate binding site for L-cysteine which leads to different chemical reaction
types.
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Selected figure(s)
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Figure 4.
Figure 4. Modelled complex
between tCGS and its substrate
HSP. The stereo plot shows the
active site of tCGS with the mod-
elled external aldimine between
HSP and PLP. The crystal structure
(blue) with the manually positioned
ligand molecule (yellow) is overlaid
with the minimised models (ligand:
grey; protein: green). The
Figure was produced with SETOR
(Evans, 1993).
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Figure 7.
Figure 7. Schematic drawing
illustrating the reaction mechanism
proposed for tCGS. After formation
of the Michaelis complex (I), trans-
aldimination leads to an external
aldimine (II); via a carbanionic
intermediate (III), a PLP substrate
ketimine (IV) is formed. After
release of the phosphate leaving
group from an a-b-unsaturated
intermediate (V), cysteine enters
the active site and reacts at C
g
of
the partitioning intermediate (qui-
ninoid form of PLP-bound vinyl-
glycine, VI). The resulting a-b-
unsaturated intermediate (VII) is
protonated to form the PLP pro-
duct ketimine (VIII). Finally, the
product PLP aldimine results from
protonation of a carbanionic inter-
mediate (IX) by the active site
lysine.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
290,
983-996)
copyright 1999.
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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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G.Jander,
and
V.Joshi
(2010).
Recent progress in deciphering the biosynthesis of aspartate-derived amino acids in plants.
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Mol Plant,
3,
54-65.
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R.Merkl,
and
M.Zwick
(2008).
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
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BMC Bioinformatics,
9,
151.
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M.J.Spiering,
C.D.Moon,
H.H.Wilkinson,
and
C.L.Schardl
(2005).
Gene clusters for insecticidal loline alkaloids in the grass-endophytic fungus Neotyphodium uncinatum.
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Genetics,
169,
1403-1414.
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M.Wirtz,
and
M.Droux
(2005).
Synthesis of the sulfur amino acids: cysteine and methionine.
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Photosynth Res,
86,
345-362.
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A.Paiardini,
F.Bossa,
and
S.Pascarella
(2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
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Protein Sci,
13,
2992-3005.
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A.Messerschmidt,
M.Worbs,
C.Steegborn,
M.C.Wahl,
R.Huber,
B.Laber,
and
T.Clausen
(2003).
Determinants of enzymatic specificity in the Cys-Met-metabolism PLP-dependent enzymes family: crystal structure of cystathionine gamma-lyase from yeast and intrafamiliar structure comparison.
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Biol Chem,
384,
373-386.
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PDB code:
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K.H.Jhee,
P.McPhie,
and
E.W.Miles
(2000).
Domain architecture of the heme-independent yeast cystathionine beta-synthase provides insights into mechanisms of catalysis and regulation.
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Biochemistry,
39,
10548-10556.
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V.Sridhar,
M.Xu,
Q.Han,
X.Sun,
Y.Tan,
R.M.Hoffman,
and
G.S.Prasad
(2000).
Crystallization and preliminary crystallographic characterization of recombinant L-methionine-alpha-deamino-gamma-mercaptomethane lyase (methioninase).
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Acta Crystallogr D Biol Crystallogr,
56,
1665-1667.
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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
code is
shown on the right.
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