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PDBsum entry 1kpf
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Protein kinase inhibitor
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PDB id
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1kpf
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* Residue conservation analysis
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Enzyme class 2:
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E.C.3.4.22.-
- ?????
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Enzyme class 3:
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E.C.3.9.1.-
- ?????
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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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DOI no:
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Science
278:286-290
(1997)
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PubMed id:
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Structure-based analysis of catalysis and substrate definition in the HIT protein family.
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C.D.Lima,
M.G.Klein,
W.A.Hendrickson.
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ABSTRACT
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The histidine triad (HIT) protein family is among the most ubiquitous and highly
conserved in nature, but a biological activity has not yet been identified for
any member of the HIT family. Fragile histidine triad protein (FHIT) and protein
kinase C interacting protein (PKCI) were used in a structure-based approach to
elucidate characteristics of in vivo ligands and reactions. Crystallographic
structures of apo, substrate analog, pentacovalent transition-state analog, and
product states of both enzymes reveal a catalytic mechanism and define substrate
characteristics required for catalysis, thus unifying the HIT family as
nucleotidyl hydrolases, transferases, or both. The approach described here may
be useful in identifying structure-function relations between protein families
identified through genomics.
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Selected figure(s)
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Figure 2.
Fig. 2. Stereo views of PKCI in (A) apo, (B) AMP-CP substrate
analog, (C) adenosine-tungstate transition-state^ analog, and
(D) AMP product-bound forms. The region shown was selected to
highlight interactions between the ligand and^ protein residues
surrounding one of the two equivalent ligand-binding sites in
the HIT homodimer. A subset of residues is shown superimposed^
on the C  backbone
cardinal spline of each respective structure. Hydrogen bonds are
denoted by dotted lines. The tryptophan shown is in the
COOH-terminal tail of the other protomer. Figure generated^ with
Setor (15).
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Figure 3.
Fig. 3. Schematic diagram of FHIT in (A) apo, (B) AMP-CP
substrate analog, (C) adenosine-tungstate transition-state^
analog, and (D) adenosine-sulfate product complexed forms. As in
Fig. 2, hydrogen-bonding interactions are depicted by dotted^
lines. A subset of residues is shown superimposed on the C backbone^
cardinal spline of each respective structure.
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The above figures are
reprinted
by permission from the AAAs:
Science
(1997,
278,
286-290)
copyright 1997.
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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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J.Martin,
M.V.St-Pierre,
and
J.F.Dufour
(2011).
Hit proteins, mitochondria and cancer.
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| |
Biochim Biophys Acta,
1807,
626-632.
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P.Tumbale,
C.D.Appel,
R.Kraehenbuehl,
P.D.Robertson,
J.S.Williams,
J.Krahn,
I.Ahel,
and
R.S.Williams
(2011).
Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.
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| |
Nat Struct Mol Biol,
18,
1189-1195.
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PDB code:
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Y.Gong,
D.Zhu,
J.Ding,
C.N.Dou,
X.Ren,
L.Gu,
T.Jiang,
and
D.C.Wang
(2011).
Crystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA.
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| |
Nat Struct Mol Biol,
18,
1297-1299.
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PDB codes:
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Y.Li,
R.Al-Eryani,
M.L.Yarbrough,
K.Orth,
and
H.L.Ball
(2011).
Characterization of AMPylation on Threonine, Serine, and Tyrosine Using Mass Spectrometry.
|
| |
J Am Soc Mass Spectrom,
22,
752-761.
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N.Tanaka,
P.Smith,
and
S.Shuman
(2010).
Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.
|
| |
Structure,
18,
449-457.
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PDB code:
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H.Banerjee,
J.B.Palenchar,
M.Lukaszewicz,
E.Bojarska,
J.Stepinski,
J.Jemielity,
A.Guranowski,
S.Ng,
D.A.Wah,
E.Darzynkiewicz,
and
V.Bellofatto
(2009).
Identification of the HIT-45 protein from Trypanosoma brucei as an FHIT protein/dinucleoside triphosphatase: substrate specificity studies on the recombinant and endogenous proteins.
|
| |
RNA,
15,
1554-1564.
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|
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R.Koike,
A.Kidera,
and
M.Ota
(2009).
Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold.
|
| |
Protein Sci,
18,
2060-2066.
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J.Kowalska,
M.Lewdorowicz,
J.Zuberek,
E.Grudzien-Nogalska,
E.Bojarska,
J.Stepinski,
R.E.Rhoads,
E.Darzynkiewicz,
R.E.Davis,
and
J.Jemielity
(2008).
Synthesis and characterization of mRNA cap analogs containing phosphorothioate substitutions that bind tightly to eIF4E and are resistant to the decapping pyrophosphatase DcpS.
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RNA,
14,
1119-1131.
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Q.Liu,
A.C.Puche,
and
J.B.Wang
(2008).
Distribution and expression of protein kinase C interactive protein (PKCI/HINT1) in mouse central nervous system (CNS).
|
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Neurochem Res,
33,
1263-1276.
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S.A.Gabel,
and
R.E.London
(2008).
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry.
|
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J Biol Inorg Chem,
13,
207-217.
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S.W.Liu,
V.Rajagopal,
S.S.Patel,
and
M.Kiledjian
(2008).
Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme.
|
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J Biol Chem,
283,
16427-16436.
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U.Rass,
I.Ahel,
and
S.C.West
(2008).
Molecular mechanism of DNA deadenylation by the neurological disease protein aprataxin.
|
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J Biol Chem,
283,
33994-34001.
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Z.Lu,
D.Dunaway-Mariano,
and
K.N.Allen
(2008).
The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.
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Proc Natl Acad Sci U S A,
105,
5687-5692.
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PDB codes:
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E.Barbier,
A.Zapata,
E.Oh,
Q.Liu,
F.Zhu,
A.Undie,
T.Shippenberg,
and
J.B.Wang
(2007).
Supersensitivity to amphetamine in protein kinase-C interacting protein/HINT1 knockout mice.
|
| |
Neuropsychopharmacology,
32,
1774-1782.
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I.Carmi,
and
E.Razin
(2007).
The role played by key transcription factors in activated mast cells.
|
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Immunol Rev,
217,
280-291.
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J.Weiske,
K.F.Albring,
and
O.Huber
(2007).
The tumor suppressor Fhit acts as a repressor of beta-catenin transcriptional activity.
|
| |
Proc Natl Acad Sci U S A,
104,
20344-20349.
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J.Zawacka-Pankau,
and
A.J.Podhajska
(2007).
Expression and simple, one-step purification of fragile histidine triad (Fhit) tumor suppressor mutant forms in Escherichia coli and their interaction with protoporphyrin IX.
|
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Biotechnol Lett,
29,
877-883.
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M.Kumar,
H.Jayaram,
R.Vasquez-Del Carpio,
X.Jiang,
Z.F.Taraporewala,
R.H.Jacobson,
J.T.Patton,
and
B.V.Prasad
(2007).
Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity.
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J Virol,
81,
12272-12284.
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PDB codes:
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U.Rass,
I.Ahel,
and
S.C.West
(2007).
Defective DNA repair and neurodegenerative disease.
|
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Cell,
130,
991.
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Y.Wei,
J.Ko,
L.F.Murga,
and
M.J.Ondrechen
(2007).
Selective prediction of interaction sites in protein structures with THEMATICS.
|
| |
BMC Bioinformatics,
8,
119.
|
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A.D.van Dijk,
and
A.M.Bonvin
(2006).
Solvated docking: introducing water into the modelling of biomolecular complexes.
|
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Bioinformatics,
22,
2340-2347.
|
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H.Li,
Y.Zhang,
T.Su,
R.M.Santella,
and
I.B.Weinstein
(2006).
Hint1 is a haplo-insufficient tumor suppressor in mice.
|
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Oncogene,
25,
713-721.
|
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I.Ahel,
U.Rass,
S.F.El-Khamisy,
S.Katyal,
P.M.Clements,
P.J.McKinnon,
K.W.Caldecott,
and
S.C.West
(2006).
The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates.
|
| |
Nature,
443,
713-716.
|
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J.Martin,
F.Magnino,
K.Schmidt,
A.C.Piguet,
J.S.Lee,
D.Semela,
M.V.St-Pierre,
A.Ziemiecki,
D.Cassio,
C.Brenner,
S.S.Thorgeirsson,
and
J.F.Dufour
(2006).
Hint2, a mitochondrial apoptotic sensitizer down-regulated in hepatocellular carcinoma.
|
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Gastroenterology,
130,
2179-2188.
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Q.Liu,
J.C.Greimann,
and
C.D.Lima
(2006).
Reconstitution, activities, and structure of the eukaryotic RNA exosome.
|
| |
Cell,
127,
1223-1237.
|
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PDB code:
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R.Vasquez-Del Carpio,
F.D.Gonzalez-Nilo,
G.Riadi,
Z.F.Taraporewala,
and
J.T.Patton
(2006).
Histidine triad-like motif of the rotavirus NSP2 octamer mediates both RTPase and NTPase activities.
|
| |
J Mol Biol,
362,
539-554.
|
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W.T.Lo,
K.H.Chin,
H.L.Shr,
F.P.Gao,
P.C.Lyu,
A.H.Wang,
and
S.H.Chou
(2006).
Crystallization and preliminary X-ray analysis of XC1015, a histidine triad-like protein from Xanthomonas campestris.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
1263-1265.
|
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F.Rodier,
R.P.Bahadur,
P.Chakrabarti,
and
J.Janin
(2005).
Hydration of protein-protein interfaces.
|
| |
Proteins,
60,
36-45.
|
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G.W.Han,
R.Schwarzenbacher,
D.McMullan,
P.Abdubek,
E.Ambing,
H.Axelrod,
T.Biorac,
J.M.Canaves,
H.J.Chiu,
X.Dai,
A.M.Deacon,
M.DiDonato,
M.A.Elsliger,
A.Godzik,
C.Grittini,
S.K.Grzechnik,
J.Hale,
E.Hampton,
J.Haugen,
M.Hornsby,
L.Jaroszewski,
H.E.Klock,
E.Koesema,
A.Kreusch,
P.Kuhn,
S.A.Lesley,
T.M.McPhillips,
M.D.Miller,
K.Moy,
E.Nigoghossian,
J.Paulsen,
K.Quijano,
R.Reyes,
G.Spraggon,
R.C.Stevens,
H.van den Bedem,
J.Velasquez,
J.Vincent,
A.White,
G.Wolf,
Q.Xu,
K.O.Hodgson,
J.Wooley,
and
I.A.Wilson
(2005).
Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution.
|
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Proteins,
60,
797-802.
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PDB code:
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Y.N.Lee,
and
E.Razin
(2005).
Nonconventional involvement of LysRS in the molecular mechanism of USF2 transcriptional activity in FcepsilonRI-activated mast cells.
|
| |
Mol Cell Biol,
25,
8904-8912.
|
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|
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|
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A.Krakowiak,
H.C.Pace,
G.M.Blackburn,
M.Adams,
A.Mekhalfia,
R.Kaczmarek,
J.Baraniak,
W.J.Stec,
and
C.Brenner
(2004).
Biochemical, crystallographic, and mutagenic characterization of hint, the AMP-lysine hydrolase, with novel substrates and inhibitors.
|
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J Biol Chem,
279,
18711-18716.
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PDB code:
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B.Z.Yuan,
A.M.Jefferson,
N.C.Popescu,
and
S.H.Reynolds
(2004).
Aberrant gene expression in human non small cell lung carcinoma cells exposed to demethylating agent 5-aza-2'-deoxycytidine.
|
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Neoplasia,
6,
412-419.
|
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J.V.Lehtonen,
D.J.Still,
V.V.Rantanen,
J.Ekholm,
D.Björklund,
Z.Iftikhar,
M.Huhtala,
S.Repo,
A.Jussila,
J.Jaakkola,
O.Pentikäinen,
T.Nyrönen,
T.Salminen,
M.Gyllenberg,
and
M.S.Johnson
(2004).
BODIL: a molecular modeling environment for structure-function analysis and drug design.
|
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J Comput Aided Mol Des,
18,
401-419.
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K.P.Parks,
H.Seidle,
N.Wright,
J.B.Sperry,
P.Bieganowski,
K.Howitz,
D.L.Wright,
and
C.Brenner
(2004).
Altered specificity of Hint-W123Q supports a role for Hint inhibition by ASW in avian sex determination.
|
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Physiol Genomics,
20,
12-14.
|
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S.W.Liu,
X.Jiao,
H.Liu,
M.Gu,
C.D.Lima,
and
M.Kiledjian
(2004).
Functional analysis of mRNA scavenger decapping enzymes.
|
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RNA,
10,
1412-1422.
|
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|
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A.Stark,
and
R.B.Russell
(2003).
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.
|
| |
Nucleic Acids Res,
31,
3341-3344.
|
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E.Koch,
W.Fiedler,
A.Tannapfel,
and
W.G.Ballhausen
(2003).
Alteration of the fragile histidine triad gene in intrahepatic cholangiocarcinoma.
|
| |
Eur J Gastroenterol Hepatol,
15,
907-913.
|
|
|
|
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|
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F.Trapasso,
A.Krakowiak,
R.Cesari,
J.Arkles,
S.Yendamuri,
H.Ishii,
A.Vecchione,
T.Kuroki,
P.Bieganowski,
H.C.Pace,
K.Huebner,
C.M.Croce,
and
C.Brenner
(2003).
Designed FHIT alleles establish that Fhit-induced apoptosis in cancer cells is limited by substrate binding.
|
| |
Proc Natl Acad Sci U S A,
100,
1592-1597.
|
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|
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J.K.Yang,
M.S.Park,
G.S.Waldo,
and
S.W.Suh
(2003).
Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis.
|
| |
Proc Natl Acad Sci U S A,
100,
455-460.
|
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PDB codes:
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N.Korsisaari,
D.J.Rossi,
K.Luukko,
K.Huebner,
M.Henkemeyer,
and
T.P.Mäkelä
(2003).
The histidine triad protein Hint is not required for murine development or Cdk7 function.
|
| |
Mol Cell Biol,
23,
3929-3935.
|
|
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|
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|
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S.D.Reid,
A.G.Montgomery,
J.M.Voyich,
F.R.DeLeo,
B.Lei,
R.M.Ireland,
N.M.Green,
M.Liu,
S.Lukomski,
and
J.M.Musser
(2003).
Characterization of an extracellular virulence factor made by group A Streptococcus with homology to the Listeria monocytogenes internalin family of proteins.
|
| |
Infect Immun,
71,
7043-7052.
|
|
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|
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T.Su,
M.Suzui,
L.Wang,
C.S.Lin,
W.Q.Xing,
and
I.B.Weinstein
(2003).
Deletion of histidine triad nucleotide-binding protein 1/PKC-interacting protein in mice enhances cell growth and carcinogenesis.
|
| |
Proc Natl Acad Sci U S A,
100,
7824-7829.
|
|
|
|
|
|
|
T.Tsujiuchi,
Y.Sasaki,
T.Kubozoe,
Y.Konishi,
and
M.Tsutsumi
(2003).
Alterations in the Fhit gene in pancreatic duct adenocarcinomas induced by N-nitrosobis(2-oxopropyl)amine in hamsters.
|
| |
Mol Carcinog,
36,
60-66.
|
|
|
|
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|
|
T.Tsujiuchi,
Y.Sasaki,
Y.Oka,
Y.Konishi,
and
M.Tsutsumi
(2003).
Fhit gene alterations in hepatocarcinogenesis induced by a choline-deficient L-amino acid-defined diet in rats.
|
| |
Mol Carcinog,
36,
147-152.
|
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|
|
|
|
C.Brenner
(2002).
Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases.
|
| |
Biochemistry,
41,
9003-9014.
|
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H.Liu,
N.D.Rodgers,
X.Jiao,
and
M.Kiledjian
(2002).
The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases.
|
| |
EMBO J,
21,
4699-4708.
|
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|
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M.Norin,
and
M.Sundström
(2002).
Structural proteomics: developments in structure-to-function predictions.
|
| |
Trends Biotechnol,
20,
79-84.
|
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M.Rubio-Texeira,
J.M.Varnum,
P.Bieganowski,
and
C.Brenner
(2002).
Control of dinucleoside polyphosphates by the FHIT-homologous HNT2 gene, adenine biosynthesis and heat shock in Saccharomyces cerevisiae.
|
| |
BMC Mol Biol,
3,
7.
|
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P.Bieganowski,
P.N.Garrison,
S.C.Hodawadekar,
G.Faye,
L.D.Barnes,
and
C.Brenner
(2002).
Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1, and Tfb3.
|
| |
J Biol Chem,
277,
10852-10860.
|
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|
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R.Lemaire,
J.Prasad,
T.Kashima,
J.Gustafson,
J.L.Manley,
and
R.Lafyatis
(2002).
Stability of a PKCI-1-related mRNA is controlled by the splicing factor ASF/SF2: a novel function for SR proteins.
|
| |
Genes Dev,
16,
594-607.
|
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|
T.Tsujiuchi,
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PDB codes:
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A.G.McLennan
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PDB codes:
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PDB code:
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PDB codes:
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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
code is
shown on the right.
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