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PDBsum entry 4fiq
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PDB id:
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Lyase
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Title:
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Crystal structure of pyridoxal biosynthesis lyase pdxs from pyrococcus horikoshii
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Structure:
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Pyridoxal biosynthesis lyase pdxs. Chain: a, b, c, d, e, f. Engineered: yes
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Source:
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Pyrococcus horikoshii. Organism_taxid: 70601. Strain: atcc 700860 / dsm 12428 / jcm 9974 / nbrc 100139 / ot-3. Gene: pdxs, ph1355. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.70Å
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R-factor:
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0.177
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R-free:
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0.246
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Authors:
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A.Matsuura,J.Y.Yoon,H.J.Yoon,H.H.Lee,S.W.Suh
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Key ref:
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A.Matsuura
et al.
(2012).
Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.
Mol Cells,
34,
407-412.
PubMed id:
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Date:
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11-Jun-12
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Release date:
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14-Nov-12
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PROCHECK
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Headers
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References
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O59080
(PDXS_PYRHO) -
Pyridoxal 5'-phosphate synthase subunit PdxS from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
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Seq:
Struc:
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335 a.a.
315 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.4.3.3.6
- pyridoxal 5'-phosphate synthase (glutamine hydrolyzing).
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Reaction:
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aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + phosphate + 3 H2O + H+
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aldehydo-D-ribose 5-phosphate
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+
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D-glyceraldehyde 3-phosphate
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+
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L-glutamine
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=
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pyridoxal 5'-phosphate
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+
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L-glutamate
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+
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phosphate
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+
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3
×
H2O
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Mol Cells
34:407-412
(2012)
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PubMed id:
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Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.
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A.Matsuura,
J.Y.Yoon,
H.J.Yoon,
H.H.Lee,
S.W.Suh.
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ABSTRACT
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Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B(6) and
is de novo synthesized from three substrates, dihydroxyacetone phosphate (DHAP),
riburose 5-phosphate (RBP), and ammonia hydrolysed from glutamine. Glutamine
amidotransferase (PdxT) catalyzes the production of ammonia from glutamine,
while PdxS catalyzes the following condensation of ribulose 5-phosphate (Ru5P),
glyceraldehyde-3-phosphate (G3P), and ammonia. PdxS exists as a hexamer or
dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus
horikoshii PdxS has a 37 amino acids insertion region, which is found in some
archaeal PdxS proteins, but its structure and function are unknown. To provide
further structural information on the role of the insertion region, the
oligomeric state, and ligand binding mode of P. horikoshii PdxS, the crystal
structure of PdxS from P. horikoshii was solved in two forms: (i) apo form, (ii)
r ibose 5-phosphate (R5P) complex and the quaternary structure of PdxS in
solution was determined by analytical gel filtration. P. horikoshii PdxS forms
hexamer in solution based on analytical gel filtration data. When we superimpose
the structure of P. horikoshii PdxS with other dodecamer structures of PdxS, the
additional insertion is located apart from the active site and induces a steric
clash on the hexamer-hexamer interface of PdxS proteins. Our results suggest
that the additional insertion perturbs dodecamer formation of P. horikoshii PdxS.
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