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PDBsum entry 1s4d
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References listed in PDB file
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Key reference
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Title
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Structure/function studies on a s-Adenosyl-L-Methionine-Dependent uroporphyrinogen III c methyltransferase (sumt), A key regulatory enzyme of tetrapyrrole biosynthesis.
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Authors
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J.Vévodová,
R.M.Graham,
E.Raux,
H.L.Schubert,
D.I.Roper,
A.A.Brindley,
A.Ian scott,
C.A.Roessner,
N.P.Stamford,
M.Elizabeth stroupe,
E.D.Getzoff,
M.J.Warren,
K.S.Wilson.
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Ref.
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J Mol Biol, 2004,
344,
419-433.
[DOI no: ]
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PubMed id
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Abstract
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The crystallographic structure of the Pseudomonas denitrificans
S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase (SUMT),
which is encoded by the cobA gene, has been solved by molecular replacement to
2.7A resolution. SUMT is a branchpoint enzyme that plays a key role in the
biosynthesis of modified tetrapyrroles by controlling flux to compounds such as
vitamin B(12) and sirohaem, and catalysing the transformation of
uroporphyrinogen III into precorrin-2. The overall topology of the enzyme is
similar to that of the SUMT module of sirohaem synthase (CysG) and the
cobalt-precorrin-4 methyltransferase CbiF and, as with the latter structures,
SUMT has the product S-adenosyl-L-homocysteine bound in the crystal. The roles
of a number of residues within the SUMT structure are discussed with respect to
their conservation either across the broader family of cobalamin biosynthetic
methyltransferases or within the sub-group of SUMT members. The D47N, L49A,
F106A, T130A, Y183A and M184A variants of SUMT were generated by mutagenesis of
the cobA gene, and tested for SAM binding and enzymatic activity. Of these
variants, only D47N and L49A bound the co-substrate S-adenosyl-L-methionine.
Consequently, all the mutants were severely restricted in their capacity to
synthesise precorrin-2, although both the D47N and L49A variants produced
significant quantities of precorrin-1, the monomethylated derivative of
uroporphyrinogen III. The activity of these variants is interpreted with respect
to the structure of the enzyme.
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Figure 4.
Figure 4. (a) Structure-based alignment of the sequences of
the transmethylase enzymes and domains from P. denitrificans
SUMT, Salmonella enterica CysG (multifunctional sirohaem
synthase) and Bacillus megaterium CbiF (anaerobic
cobalt-precorrin-4 methyltransferase) with the secondary
structure labelled. The 3D alignment was performed using the SSM
protein structure matching web page
(http://www.ebi.ac.uk/msd-srv/ssm). The residues indicated with
cyan dotted lines are either not modelled in the electron
density or excluded from the alignment by SSM as being too far
apart to be considered equivalent. (b) Superposition of the
SUMT, CysG and CbiF molecules including SAH. The position of the
ligand is almost identical in the three molecules. SUMT is
coloured cyan, CysG magenta and CbiF yellow (all including their
ligands).
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Figure 5.
Figure 5. (a) SAH binding by surrounding (2.6-3.8 Å)
residues is shown. Residues highlighted in the Figure interact
directly with SAH either by H-bonds or by van der Waals
contacts. (b) Molecule of SAH. 1s electron density from a 2F[o]
-F[c] map contoured in blue.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
344,
419-433)
copyright 2004.
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