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References listed in PDB file
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Key reference
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Title
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Unique utilization of a phosphoprotein phosphatase fold by a mammalian phosphodiesterase associated with wagr syndrome.
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Authors
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U.Dermol,
V.Janardan,
R.Tyagi,
S.S.Visweswariah,
M.Podobnik.
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Ref.
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J Mol Biol, 2011,
412,
481-494.
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PubMed id
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Abstract
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No abstract given.
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Secondary reference #1
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Title
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Characterization of an evolutionarily conserved metallophosphoesterase that is expressed in the fetal brain and associated with the wagr syndrome.
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Authors
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R.Tyagi,
A.R.Shenoy,
S.S.Visweswariah.
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Ref.
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J Biol Chem, 2009,
284,
5217-5228.
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PubMed id
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Secondary reference #2
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Title
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A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability.
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Authors
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M.Podobnik,
R.Tyagi,
N.Matange,
U.Dermol,
A.K.Gupta,
R.Mattoo,
K.Seshadri,
S.S.Visweswariah.
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Ref.
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J Biol Chem, 2009,
284,
32846-32857.
[DOI no: ]
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PubMed id
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Figure 1.
Crystal structure of the Rv08051-318 homodimer. A, ribbon
representation of the Rv08051-318 dimer. The MPE catalytic
core is colored light gray (left-side protomer) or dark gray
(right-side protomer). New structural elements are colored
orange (attached to the dark gray catalytic core) or green
(attached to the light gray catalytic core). N and C termini of
the dark gray/orange protomer are marked. α-Helices and
β-sheets are indicated, dark gray/orange protomer with a prime.
Active site metals ions are shown as spheres: Fe3+, cyan;
Mn2+, magenta. B, Rv08051-318 monomer: catalytic core, dark
gray; new structural elements, orange. Active site metals are
shown as in A. C, secondary structure elements of Rv08051-318
monomer superimposed onto the amino acid sequence (β-strands,
yellow arrows; α-helices, red cylinders). Newly defined parts
of the Rv08051-318 structure are in green. Highly conserved
MPE family regions are highlighted by cyan boxes and several
residues indicated in the text are numbered. Small letters
represent parts of the structure that are not defined by
electron density. D, polar interactions: between N-terminal and
C-terminal residues of the same protomer (black dashed lines);
between N-terminal peptide of one protomer and residues of the
other protomer (red dashed line). Residues of the protomer in
dark gray/orange combination are marked with a prime (i.e.
D′187) and the light gray/green protomer as normal (i.e. D13).
E, swapped structural elements between the protomers in the
Rv08051-318 dimer. Color code is the same as in A. Protomer
colored dark gray/orange is shown as a surface and the light
gray/green protomer as ribbon.
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Figure 3.
The active site of Rv0805. A, comparison of Rv08051-278
(left) and Rv08051-318 (right) dimer shows a significant
closure of the active site in Rv08051-318. In this view, only
one of the two equal active sites is seen (light gray/green
protomer). Yellow rectangles cover the regions of residues
Glu′270-Pro′278 that run into α′7 helix from the bottom
up. B, Rv08051-318 active site with bound 5′-AMP (left
panel). 5′-AMP is shown as sticks (carbon, yellow; oxygen,
red; nitrogen, blue; phosphorus, orange). Middle panel, zoom of
the active site. C, zoom of the active site showing acetate in
sticks bound to Rv08051-318 (carbon, yellow; oxygen, red;
spheres are Fe3+, cyan; Mn2+, magenta; planar active site
water, red). D, 5′-AMP-Rv08051-318 complex. For the
5′-AMP complex, polar interactions with the active site
residues, metals, and water molecules are shown. Color code is
the same as described in the legend to Fig. 1, residues of the
protomer in dark gray/orange combination are marked with a prime.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #3
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Title
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Structural and biochemical analysis of the rv0805 cyclic nucleotide phosphodiesterase from mycobacterium tuberculosis.
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Authors
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A.R.Shenoy,
M.Capuder,
P.Draskovic,
D.Lamba,
S.S.Visweswariah,
M.Podobnik.
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Ref.
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J Mol Biol, 2007,
365,
211-225.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. The Rv0805 dimer.
(a) Rv08051–278 protomers (yellow and grey) dimerize
in a manner that places one active site on each side of the
dimer. Metals are represented by labeled spheres and phosphate (P,
orange; O, red) and residues proximal to the dimer interface by sticks
(C, green; N, blue; O, red). The planar water is rendered as a red
sphere. The 2-fold crystallographic axis is marked by a dotted
line. (b) The extended 11-stranded β-sheet in the
Rv08051–278 formed by the juxtapositioning of the
five and six-stranded sheets from the two protomers is shown. The
front sheet is colored in red and the back sheet is shown in
grey. Other regions of the protein have been omitted for clarity. (c)
The interfacial residues in Rv08051–278, rendered as
sticks (C, yellow for protomer A and grey for protomer B; N, blue; O,
red), showing inter-protomer polar interactions (dotted lines). The
view is  45° rotated to the right
around the axis shown in (a).
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Figure 3.
Figure 3. The Rv0805 active site.
(a) The stereo view of the active site of wild-type
Rv08051–278 is shown with bound metals and
phosphate. Residues are rendered as sticks (C, grey; N, blue; O, red;
P, orange) and the metals as spheres. The red sphere is the planar
water molecule. Polar interactions between the side-chains of Asp66
and His23, Asn97 and His140 and the octahedral co-ordination of both
metals are shown as dotted lines. The
Fo–Fc electron density map
around the phosphate is contoured at 3σ (red) and 5σ
(cyan). (b) Active site of the
Rv08051–278D66A mutant with bound metals
and cacodylate (C, orange; As, purple) is shown. The amino acid
residues of the polypeptide are colored by atom types (C, grey; N,
blue; O, red; P, orange) and the planar water is shown as a red
sphere. The Fo–Fc electron
density map around the cacodylate is contoured at 3σ (red) and
5σ (cyan). (c) Overlay of the active site of
Rv08051–278 (grey ribbon; C, grey; N, blue; O, red;
P, orange) and PP1 (PDB code 1FJM; green ribbon; C, green; N, blue; O,
red) showing the difference in the orientation of Asp66 in Rv0805 in
comparison to the corresponding residue (Asp95) in PP1. Residues are
labeled in blue for Rv0805 and green for PP1.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #4
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Title
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The rv0805 gene from mycobacterium tuberculosis encodes a 3',5'-Cyclic nucleotide phosphodiesterase: biochemical and mutational analysis.
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Authors
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A.R.Shenoy,
N.Sreenath,
M.Podobnik,
M.Kovacevic,
S.S.Visweswariah.
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Ref.
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Biochemistry, 2005,
44,
15695-15704.
[DOI no: ]
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PubMed id
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