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PDBsum entry 1b9h
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Rifamycin biosynthesis (rifd gene)
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PDB id
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1b9h
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Contents |
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* Residue conservation analysis
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Enzyme class 1:
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E.C.2.6.1.-
- ?????
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Enzyme class 2:
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E.C.4.2.1.144
- 3-amino-5-hydroxybenzoate synthase.
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Reaction:
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5-deoxy-5-amino-3-dehydroshikimate = 3-amino-5-hydroxybenzoate + H2O + H+
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Cofactor:
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Pyridoxal 5'-phosphate
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Pyridoxal 5'-phosphate
Bound ligand (Het Group name =
PLP)
matches with 93.75% similarity
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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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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Biochemistry
38:9840-9849
(1999)
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PubMed id:
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Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase.
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J.C.Eads,
M.Beeby,
G.Scapin,
T.W.Yu,
H.G.Floss.
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ABSTRACT
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The biosynthesis of ansamycin antibiotics, including rifamycin B, involves the
synthesis of an aromatic precursor, 3-amino-5-hydroxybenzoic acid (AHBA), which
serves as starter for the assembly of the antibiotics' polyketide backbone. The
terminal enzyme of AHBA formation, AHBA synthase, is a dimeric, pyridoxal
5'-phosphate (PLP) dependent enzyme with pronounced sequence homology to a
number of PLP enzymes involved in the biosynthesis of antibiotic sugar moieties.
The structure of AHBA synthase from Amycolatopsis mediterranei has been
determined to 2.0 A resolution, with bound cofactor, PLP, and in a complex with
PLP and an inhibitor (gabaculine). The overall fold of AHBA synthase is similar
to that of the aspartate aminotransferase family of PLP-dependent enzymes, with
a large domain containing a seven-stranded beta-sheet surrounded by
alpha-helices and a smaller domain consisting of a four-stranded antiparallel
beta-sheet and four alpha-helices. The uninhibited form of the enzyme shows the
cofactor covalently linked to Lys188 in an internal aldimine linkage. On binding
the inhibitor, gabaculine, the internal aldimine linkage is broken, and a
covalent bond is observed between the cofactor and inhibitor. The active site is
composed of residues from two subunits of AHBA synthase, indicating that AHBA
synthase is active as a dimer.
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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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H.G.Floss,
T.W.Yu,
and
K.Arakawa
(2011).
The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC(7)N units in ansamycin and mitomycin antibiotics: a review.
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J Antibiot (Tokyo),
64,
35-44.
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P.Smith,
P.H.Szu,
C.Bui,
H.W.Liu,
and
S.C.Tsai
(2008).
Structure and mutagenic conversion of E1 dehydrase: at the crossroads of dehydration, amino transfer, and epimerization.
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Biochemistry,
47,
6329-6341.
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F.Kudo,
Y.Kasama,
T.Hirayama,
and
T.Eguchi
(2007).
Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation.
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J Antibiot (Tokyo),
60,
492-503.
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Q.Wu,
Y.N.Liu,
H.Chen,
E.J.Molitor,
and
H.W.Liu
(2007).
A retro-evolution study of CDP-6-deoxy-D-glycero-L-threo-4-hexulose-3-dehydrase (E1) from Yersinia pseudotuberculosis: implications for C-3 deoxygenation in the biosynthesis of 3,6-dideoxyhexoses.
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Biochemistry,
46,
3759-3767.
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B.Popovic,
X.Tang,
D.Y.Chirgadze,
F.Huang,
T.L.Blundell,
and
J.B.Spencer
(2006).
Crystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis.
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Proteins,
65,
220-230.
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PDB codes:
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P.D.Cook,
J.B.Thoden,
and
H.M.Holden
(2006).
The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme.
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Protein Sci,
15,
2093-2106.
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PDB codes:
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S.Vijayakumar,
A.Merkx-Jacques,
D.B.Ratnayake,
I.Gryski,
R.K.Obhi,
S.Houle,
C.M.Dozois,
and
C.Creuzenet
(2006).
Cj1121c, a novel UDP-4-keto-6-deoxy-GlcNAc C-4 aminotransferase essential for protein glycosylation and virulence in Campylobacter jejuni.
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J Biol Chem,
281,
27733-27743.
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R.K.Obhi,
and
C.Creuzenet
(2005).
Biochemical characterization of the Campylobacter jejuni Cj1294, a novel UDP-4-keto-6-deoxy-GlcNAc aminotransferase that generates UDP-4-amino-4,6-dideoxy-GalNAc.
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J Biol Chem,
280,
20902-20908.
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T.E.Carver,
B.Bordeau,
M.D.Cummings,
E.C.Petrella,
M.J.Pucci,
L.E.Zawadzke,
B.A.Dougherty,
J.A.Tredup,
J.W.Bryson,
J.Yanchunas,
M.L.Doyle,
M.R.Witmer,
M.I.Nelen,
R.L.DesJarlais,
E.P.Jaeger,
H.Devine,
E.D.Asel,
B.A.Springer,
R.Bone,
F.R.Salemme,
and
M.J.Todd
(2005).
Decrypting the biochemical function of an essential gene from Streptococcus pneumoniae using ThermoFluor technology.
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J Biol Chem,
280,
11704-11712.
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J.M.Cassady,
K.K.Chan,
H.G.Floss,
and
E.Leistner
(2004).
Recent developments in the maytansinoid antitumor agents.
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Chem Pharm Bull (Tokyo),
52,
1.
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A.Pfoestl,
A.Hofinger,
P.Kosma,
and
P.Messner
(2003).
Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose in Aneurinibacillus thermoaerophilus L420-91T.
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J Biol Chem,
278,
26410-26417.
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K.Watanabe,
M.A.Rude,
C.T.Walsh,
and
C.Khosla
(2003).
Engineered biosynthesis of an ansamycin polyketide precursor in Escherichia coli.
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Proc Natl Acad Sci U S A,
100,
9774-9778.
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S.D.Breazeale,
A.A.Ribeiro,
and
C.R.Raetz
(2003).
Origin of lipid A species modified with 4-amino-4-deoxy-L-arabinose in polymyxin-resistant mutants of Escherichia coli. An aminotransferase (ArnB) that generates UDP-4-deoxyl-L-arabinose.
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J Biol Chem,
278,
24731-24739.
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B.W.Noland,
J.M.Newman,
J.Hendle,
J.Badger,
J.A.Christopher,
J.Tresser,
M.D.Buchanan,
T.A.Wright,
M.E.Rutter,
W.E.Sanderson,
H.J.Müller-Dieckmann,
K.S.Gajiwala,
and
S.G.Buchanan
(2002).
Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme.
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Structure,
10,
1569-1580.
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PDB codes:
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J.Sandmark,
S.Mann,
A.Marquet,
and
G.Schneider
(2002).
Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin.
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J Biol Chem,
277,
43352-43358.
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PDB codes:
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R.Contestabile,
A.Paiardini,
S.Pascarella,
M.L.di Salvo,
S.D'Aguanno,
and
F.Bossa
(2001).
l-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase. A subgroup of strictly related enzymes specialized for different functions.
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Eur J Biochem,
268,
6508-6525.
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G.Schneider,
H.Käck,
and
Y.Lindqvist
(2000).
The manifold of vitamin B6 dependent enzymes.
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Structure,
8,
R1-R6.
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R.Lal,
R.Kumari,
H.Kaur,
R.Khanna,
N.Dhingra,
and
D.Tuteja
(2000).
Regulation and manipulation of the gene clusters encoding type-I PKSs.
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Trends Biotechnol,
18,
264-274.
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H.G.Floss,
and
T.W.Yu
(1999).
Lessons from the rifamycin biosynthetic gene cluster.
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Curr Opin Chem Biol,
3,
592-597.
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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
