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PDBsum entry 1vrm
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Biosynthetic protein
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PDB id
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1vrm
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.7.1.180
- FAD:protein Fmn transferase.
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Reaction:
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L-threonyl-[protein] + FAD = FMN-L-threonyl-[protein] + AMP + H+
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L-threonyl-[protein]
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+
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FAD
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=
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FMN-L-threonyl-[protein]
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+
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AMP
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+
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H(+)
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Cofactor:
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Mg(2+)
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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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Proteins
64:1083-1090
(2006)
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PubMed id:
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Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution.
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G.W.Han,
S.Sri Krishna,
R.Schwarzenbacher,
D.McMullan,
K.Ginalski,
M.A.Elsliger,
S.M.Brittain,
P.Abdubek,
S.Agarwalla,
E.Ambing,
T.Astakhova,
H.Axelrod,
J.M.Canaves,
H.J.Chiu,
M.DiDonato,
S.K.Grzechnik,
J.Hale,
E.Hampton,
J.Haugen,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
E.Koesema,
A.Kreusch,
P.Kuhn,
M.D.Miller,
A.T.Morse,
K.Moy,
E.Nigoghossian,
S.Oommachen,
J.Ouyang,
J.Paulsen,
K.Quijano,
R.Reyes,
C.Rife,
G.Spraggon,
R.C.Stevens,
H.van den Bedem,
J.Velasquez,
X.Wang,
B.West,
A.White,
G.Wolf,
Q.Xu,
K.O.Hodgson,
J.Wooley,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
I.A.Wilson.
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ABSTRACT
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Selected figure(s)
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Figure 1.
Figure 1. Crystal structure of TM1553. A: Ribbon drawing where
the N-terminal domain (cyan), helical domain (pink), linker
region (slate-blue), and C-terminal domain (yellow) are colored
to illustrate the domain organization. Helices (H1-H12) and  -strands
( 1-
15)
are labeled, and the unknown ligand is represented as orange
spheres. B: Diagram showing the secondary structural elements in
TM1553 superimposed on its primary sequence. The  -helices,
3[10]-helices, -strands
(indicated by red A, B, C, and D to represent the -sheet
designation), -bulges,
and  -turns
are indicated. The -hairpins
are depicted as red loops. Dashed lines indicate that no
electron density was observed for that region.
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Figure 2.
Figure 2. A: Structural diagram of the monomeric unit of
uricase (PDB 1r51), which is also composed of a tandem
duplication of the T-fold. The N- and C-terminal domains are
colored green and gray, respectively. B: Tunnel-shaped
oligomeric complex of uricase. The active site is composed of
residues from different subunits (colored gray, beige, green,
and slate-blue) of the enzyme. The ligand molecules bound at the
active sites are shown in CPK. C: Stereo diagram of the
structure alignment of the monomeric unit of uricase and TM1553.
TM1553 is colored blue and uricase gray. Uricase does not
contain the additional helical domain. The ligands at the active
sites of uricase (shown in CPK) and TM1553 (shown as orange
spheres) are in completely different locations. D: Stereo
diagram of the putative active site of TM1553. The structure of
TM1553 is colored gray and the side-chains of residues within a
4 Å shell of the UNL are displayed in ball-and-stick
representation. The electron density of a 2Fo-Fc omit map
contoured at 1  (blue)
around the UNL (orange spheres) in the active site is shown.
Water molecules in the active site are not displayed.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2006,
64,
1083-1090)
copyright 2006.
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Figures were
selected
by an automated process.
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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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T.C.Terwilliger,
P.D.Adams,
R.J.Read,
A.J.McCoy,
N.W.Moriarty,
R.W.Grosse-Kunstleve,
P.V.Afonine,
P.H.Zwart,
and
L.W.Hung
(2009).
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
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Acta Crystallogr D Biol Crystallogr,
65,
582-601.
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C.J.McCleverty,
L.Columbus,
A.Kreusch,
and
S.A.Lesley
(2008).
Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634.
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Protein Sci,
17,
869-877.
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PDB codes:
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Citation data come partly from CiteXplore and partly
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Where a reference describes a PDB structure, the PDB
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shown on the right.
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