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PDBsum entry 4iyo
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PDB id:
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Lyase
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Title:
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Crystal structure of cystathionine gamma lyase from xanthomonas oryzae pv. Oryzae (xometc) in complex with e-site serine, a-site serine, a- site external aldimine structure with aminoacrylate and a-site iminopropionate intermediates
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Structure:
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Cystathionine gamma-lyase-like protein. Chain: a. Engineered: yes. Cystathionine gamma-lyase-like protein, lys201a modified. Chain: b, c, d. Engineered: yes
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Source:
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Xanthomonas oryzae pv. Oryzae. Organism_taxid: 291331. Strain: kacc 10331/kxo85. Gene: metb, xocgl, xoo0778. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
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Resolution:
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1.80Å
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R-factor:
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0.138
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R-free:
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0.180
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Authors:
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H.P.T.Ngo,J.K.Kim,L.W.Kang
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Key ref:
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H.P.Ngo
et al.
(2014).
PLP undergoes conformational changes during the course of an enzymatic reaction.
Acta Crystallogr D Biol Crystallogr,
70,
596-606.
PubMed id:
DOI:
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Date:
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29-Jan-13
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Release date:
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29-Jan-14
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PROCHECK
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Headers
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References
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Q5H4T8
(Q5H4T8_XANOR) -
Cystathionine gamma-lyase-like protein from Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)
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Seq:
Struc:
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397 a.a.
381 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.4.4.1.1
- cystathionine gamma-lyase.
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Reaction:
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L,L-cystathionine + H2O = 2-oxobutanoate + L-cysteine + NH4+
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L,L-cystathionine
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+
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H2O
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=
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2-oxobutanoate
Bound ligand (Het Group name = )
matches with 85.71% similarity
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+
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L-cysteine
Bound ligand (Het Group name = )
matches with 75.00% similarity
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+
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NH4(+)
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Cofactor:
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Pyridoxal 5'-phosphate
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Pyridoxal 5'-phosphate
Bound ligand (Het Group name =
0JO)
matches with 68.18% similarity
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Acta Crystallogr D Biol Crystallogr
70:596-606
(2014)
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PubMed id:
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PLP undergoes conformational changes during the course of an enzymatic reaction.
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H.P.Ngo,
N.M.Cerqueira,
J.K.Kim,
M.K.Hong,
P.A.Fernandes,
M.J.Ramos,
L.W.Kang.
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ABSTRACT
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Numerous enzymes, such as the pyridoxal 5'-phosphate (PLP)-dependent enzymes,
require cofactors for their activities. Using X-ray crystallography, structural
snapshots of the L-serine dehydratase catalytic reaction of a bacterial
PLP-dependent enzyme were determined. In the structures, the dihedral angle
between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to
52°. It is proposed that the organic cofactor PLP directly catalyzes reactions
by active conformational changes, and the novel catalytic mechanism involving
the PLP cofactor was confirmed by high-level quantum-mechanical calculations.
The conformational change was essential for nucleophilic attack of the substrate
on PLP, for concerted proton transfer from the substrate to the protein and for
directing carbanion formation of the substrate. Over the whole catalytic cycle,
the organic cofactor catalyzes a series of reactions, like the enzyme. The
conformational change of the PLP cofactor in catalysis serves as a starting
point for identifying the previously unknown catalytic roles of organic
cofactors.
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