 |
PDBsum entry 1k3r
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Structural genomics, unknown function
|
PDB id
|
|
|
|
1k3r
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Structural genomics, unknown function
|
|
|
Title:
|
|
Crystal structure of the methyltransferase with a knot from methanobacterium thermoautotrophicum
|
|
Structure:
|
|
Conserved protein mt0001. Chain: a, b. Engineered: yes
|
|
Source:
|
|
Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
|
|
Biol. unit:
|
|
Dimer (from PDB file)
|
|
Resolution:
|
|
|
2.30Å
|
R-factor:
|
0.221
|
R-free:
|
0.277
|
|
|
Authors:
|
|
T.I.Zarembinski,Y.Kim,K.Peterson,D.Christendat,A.Dharamsi, C.H.Arrowsmith,A.M.Edwards,A.Joachimiak,Midwest Center For Structural Genomics (Mcsg)
|
Key ref:
|
|
T.I.Zarembinski
et al.
(2003).
Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
Proteins,
50,
177-183.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
03-Oct-01
|
Release date:
|
15-May-02
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
O26109
(O26109_METTH) -
Conserved protein from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
|
|
|
|
Seq:
Struc:
|
|
|
|
268 a.a.
262 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Proteins
50:177-183
(2003)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
|
|
T.I.Zarembinski,
Y.Kim,
K.Peterson,
D.Christendat,
A.Dharamsi,
C.H.Arrowsmith,
A.M.Edwards,
A.Joachimiak.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 4.
Figure 4. C[  ]trace
and stereo view of MT1-DD and MT1-CSD structural overlap. (a)
The MT1-DD (red) is shown overlapped with the corresponding
domain of MTHFR (green). Corresponding  -helices
and  -strands
are labeled as and
,
respectively, according to numbering convention for MTHFR. (b)
The small domain of MT1 (red) is shown overlapped with 1SRO
(green), 1MJC (blue), and 1FJF_Q (orange). Figures were prepared
with the program MOLSCRIPT.^33 Residues were deleted from
proteins where appropriate to simplify the diagram. Refer to
text for PDB identifiers.
|
|
Figure 5.
Figure 5. The MT1 trefoil knot. Residues 1-190 and 199-229 are
shown in solvent accessible surface representation (1.4 Å
radius). The knot loop (residues 191-198) is in blue and the
polypeptide chain threaded through the loop (residues 230-264)
is labeled red. Crossover residues (Ser194 and Asn234) as well
as Arg191 on the loop, Trp232 and Glu239 on threaded through
chain are marked as a reference points. Carboxy terminus is
labeled  C
 .
Figure was prepared with WebLabPro.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2003,
50,
177-183)
copyright 2003.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.Ochi,
K.Makabe,
K.Kuwajima,
and
H.Hori
(2010).
Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes.
|
| |
J Biol Chem,
285,
9018-9029.
|
|
|
|
|
|
|
S.Arragain,
R.Garcia-Serres,
G.Blondin,
T.Douki,
M.Clemancey,
J.M.Latour,
F.Forouhar,
H.Neely,
G.T.Montelione,
J.F.Hunt,
E.Mulliez,
M.Fontecave,
and
M.Atta
(2010).
Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.
|
| |
J Biol Chem,
285,
5792-5801.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.L.Mallam
(2009).
How does a knotted protein fold?
|
| |
FEBS J,
276,
365-375.
|
|
|
|
|
|
|
F.Forouhar,
A.Kuzin,
J.Seetharaman,
I.Lee,
W.Zhou,
M.Abashidze,
Y.Chen,
W.Yong,
H.Janjua,
Y.Fang,
D.Wang,
K.Cunningham,
R.Xiao,
T.B.Acton,
E.Pichersky,
D.F.Klessig,
C.W.Porter,
G.T.Montelione,
and
L.Tong
(2007).
Functional insights from structural genomics.
|
| |
J Struct Funct Genomics,
8,
37-44.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.L.Tkaczuk,
S.Dunin-Horkawicz,
E.Purta,
and
J.M.Bujnicki
(2007).
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
|
| |
BMC Bioinformatics,
8,
73.
|
|
|
|
|
|
|
S.Wallin,
K.B.Zeldovich,
and
E.I.Shakhnovich
(2007).
The folding mechanics of a knotted protein.
|
| |
J Mol Biol,
368,
884-893.
|
|
|
|
|
|
|
K.Watanabe,
O.Nureki,
S.Fukai,
Y.Endo,
and
H.Hori
(2006).
Functional categorization of the conserved basic amino acid residues in TrmH (tRNA (Gm18) methyltransferase) enzymes.
|
| |
J Biol Chem,
281,
34630-34639.
|
|
|
|
|
|
|
J.R.Wagner,
J.S.Brunzelle,
K.T.Forest,
and
R.D.Vierstra
(2005).
A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.
|
| |
Nature,
438,
325-331.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Watanabe,
O.Nureki,
S.Fukai,
R.Ishii,
H.Okamoto,
S.Yokoyama,
Y.Endo,
and
H.Hori
(2005).
Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family.
|
| |
J Biol Chem,
280,
10368-10377.
|
|
|
|
|
|
|
M.H.Renalier,
N.Joseph,
C.Gaspin,
P.Thebault,
and
A.Mougin
(2005).
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.
|
| |
RNA,
11,
1051-1063.
|
|
|
|
|
|
|
A.F.Yakunin,
A.A.Yee,
A.Savchenko,
A.M.Edwards,
and
C.H.Arrowsmith
(2004).
Structural proteomics: a tool for genome annotation.
|
| |
Curr Opin Chem Biol,
8,
42-48.
|
|
|
|
|
|
|
S.Hovmöller,
and
T.Zhou
(2004).
Why are both ends of the polypeptide chain on the outside of proteins?
|
| |
Proteins,
55,
219-222.
|
|
|
|
|
|
|
Y.Ye,
and
A.Godzik
(2004).
Database searching by flexible protein structure alignment.
|
| |
Protein Sci,
13,
1841-1850.
|
|
|
|
|
|
|
F.Forouhar,
J.Shen,
R.Xiao,
T.B.Acton,
G.T.Montelione,
and
L.Tong
(2003).
Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot.
|
| |
Proteins,
53,
329-332.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.J.Ahn,
H.W.Kim,
H.J.Yoon,
B.I.Lee,
S.W.Suh,
and
J.K.Yang
(2003).
Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.
|
| |
EMBO J,
22,
2593-2603.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.A.Kurowski,
J.M.Sasin,
M.Feder,
J.Debski,
and
J.M.Bujnicki
(2003).
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.
|
| |
BMC Bioinformatics,
4,
9.
|
|
|
|
|
|
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.
|
|
Links
