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Contents |
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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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Yeast 5-aminolaevulinic acid dehydratase putative cyclic reaction intermediate complex
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Structure:
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Delta-aminolevulinic acid dehydratase. Chain: a. Synonym: aladh, porphobilinogen synthase. Engineered: yes. Other_details: co-crystallisation with substrate aminolaevulinic acid
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Source:
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Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: ns1(jm109/pns1). Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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Octamer (from PDB file)
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Resolution:
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1.6Å
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R-factor:
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0.188
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R-free:
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0.241
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Authors:
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P.T.Erskine,L.Coates,D.Butler,J.H.Youell,A.A.Brindley, S.P.Wood,M.J.Warren,P.M.Shoolingin-Jordan,J.B.Cooper
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Key ref:
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P.T.Erskine
et al.
(2003).
X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase.
Biochem J,
373,
733-738.
PubMed id:
DOI:
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Date:
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27-May-03
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Release date:
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02-Jun-03
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PROCHECK
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Headers
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References
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P05373
(HEM2_YEAST) -
Delta-aminolevulinic acid dehydratase
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Seq:
Struc:
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342 a.a.
340 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.4.2.1.24
- Porphobilinogen synthase.
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Pathway:
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Porphyrin Biosynthesis (early stages)
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Reaction:
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2 5-aminolevulinate = porphobilinogen + 2 H2O
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2
×
5-aminolevulinate
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=
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porphobilinogen
Bound ligand (Het Group name = )
corresponds exactly
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+
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2
×
H(2)O
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Cofactor:
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Zinc
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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2 terms
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Biological process
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metabolic process
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4 terms
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Biochemical function
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catalytic activity
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8 terms
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DOI no:
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Biochem J
373:733-738
(2003)
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PubMed id:
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X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase.
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P.T.Erskine,
L.Coates,
D.Butler,
J.H.Youell,
A.A.Brindley,
S.P.Wood,
M.J.Warren,
P.M.Shoolingin-Jordan,
J.B.Cooper.
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ABSTRACT
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The X-ray structure of yeast 5-aminolaevulinic acid dehydratase, in which the
catalytic site of the enzyme is complexed with a putative cyclic intermediate
composed of both substrate moieties, has been solved at 0.16 nm (1.6 A)
resolution. The cyclic intermediate is bound covalently to Lys(263) with the
amino group of the aminomethyl side chain ligated to the active-site zinc ion in
a position normally occupied by a catalytic hydroxide ion. The cyclic
intermediate is catalytically competent, as shown by its turnover in the
presence of added substrate to form porphobilinogen. The findings, combined with
those of previous studies, are consistent with a catalytic mechanism in which
the C-C bond linking both substrates in the intermediate is formed before the
C-N bond.
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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.Layer,
J.Reichelt,
D.Jahn,
and
D.W.Heinz
(2010).
Structure and function of enzymes in heme biosynthesis.
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Protein Sci, 19,
1137-1161.
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A.Gumm,
A.Hammershøi,
M.Kofod-Hansen,
O.Mønsted,
and
H.Osholm Sørensen
(2007).
First aminoacetone chelate: [Co(tren){NH2CH2C(O)CH3}]3+-a substrate binding and activation model for zinc(II)-dependent 5-aminolaevulinic acid dehydratase.
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Dalton Trans, 0,
3227-3231.
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L.Coates,
G.Beaven,
P.T.Erskine,
S.I.Beale,
S.P.Wood,
P.M.Shoolingin-Jordan,
and
J.B.Cooper
(2005).
Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor.
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Acta Crystallogr D Biol Crystallogr, 61,
1594-1598.
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PDB code:
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L.Tang,
L.Stith,
and
E.K.Jaffe
(2005).
Substrate-induced interconversion of protein quaternary structure isoforms.
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J Biol Chem, 280,
15786-15793.
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P.T.Erskine,
L.Coates,
R.Newbold,
A.A.Brindley,
F.Stauffer,
G.D.Beaven,
R.Gill,
A.Coker,
S.P.Wood,
M.J.Warren,
P.M.Shoolingin-Jordan,
R.Neier,
and
J.B.Cooper
(2005).
Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid.
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Acta Crystallogr D Biol Crystallogr, 61,
1222-1226.
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PDB code:
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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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Links
