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PDBsum entry 1vig
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Ribonucleoprotein
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PDB id
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1vig
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Contents |
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* Residue conservation analysis
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PDB id:
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Ribonucleoprotein
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Title:
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Nmr study of vigilin, repeat 6, 40 structures
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Structure:
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Vigilin. Chain: a. Fragment: kh6, residues 432 to 501. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Gene: human vigilin sixth kh repeat. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: n-terminal 6-histidine fusion protein yes
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NMR struc:
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40 models
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Authors:
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G.Musco,G.Stier,C.Joseph,M.A.C.Morelli,M.Nilges,T.J.Gibson,A.Pastore
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Key ref:
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G.Musco
et al.
(1996).
Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.
Cell,
85,
237-245.
PubMed id:
DOI:
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Date:
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29-Nov-95
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Release date:
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03-Apr-96
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PROCHECK
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Headers
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References
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Q00341
(VIGLN_HUMAN) -
Vigilin from Homo sapiens
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Seq:
Struc:
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1268 a.a.
71 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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DOI no:
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Cell
85:237-245
(1996)
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PubMed id:
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Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome.
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G.Musco,
G.Stier,
C.Joseph,
M.A.Castiglione Morelli,
M.Nilges,
T.J.Gibson,
A.Pastore.
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ABSTRACT
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The KH module is a sequence motif found in a number of proteins that are known
to be in close association with RNA. Experimental evidence suggests a direct
involvement of KH in RNA binding. The human FMR1 protein, which has two KH
domains, is associated with fragile X syndrome, the most common inherited cause
of mental retardation. Here we present the three-dimensional solution structure
of the KH module. The domain consists of a stable beta alpha alpha beta beta
alpha fold. On the basis of our results, we suggest a potential surface for RNA
binding centered on the loop between the first two helices. Substitution of a
well-conserved hydrophobic residue located on the second helix destroys the KH
fold; a mutation of this position in FMR1 leads to an aggravated fragile X
phenotype.
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Selected figure(s)
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Figure 4.
Figure 4. Suggested Surface for RNA RecognitionMOLSCRIPT
representation of the Vig-6 domain, showing conserved positive
charges (light blue) and the backbone of the GkxG loop (yellow).
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Figure 5.
Figure 5. Models of the Two KH Repeats of FMR1Models are
based on the coordinates of the Vig-6 average structure and the
new sequence alignment (Figure 3). Coloring is as follows:
magenta, the backbone atoms; green, the hydrophobic side chains;
yellow, the position affected by the mutation (isoleucine to
asparagine) at residues Ile-241 and Ile-304) of the FMR1 protein.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1996,
85,
237-245)
copyright 1996.
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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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L.Sjekloća,
K.Pauwels,
and
A.Pastore
(2011).
On the aggregation properties of FMRP - a link with the FXTAS syndrome?
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FEBS J,
278,
1912-1921.
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A.Chaudhury,
P.Chander,
and
P.H.Howe
(2010).
Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: Focus on hnRNP E1's multifunctional regulatory roles.
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RNA,
16,
1449-1462.
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A.Rybarska,
M.Harterink,
B.Jedamzik,
A.P.Kupinski,
M.Schmid,
and
C.R.Eckmann
(2009).
GLS-1, a novel P granule component, modulates a network of conserved RNA regulators to influence germ cell fate decisions.
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PLoS Genet,
5,
e1000494.
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J.B.Zang,
E.D.Nosyreva,
C.M.Spencer,
L.J.Volk,
K.Musunuru,
R.Zhong,
E.F.Stone,
L.A.Yuva-Paylor,
K.M.Huber,
R.Paylor,
J.C.Darnell,
and
R.B.Darnell
(2009).
A mouse model of the human Fragile X syndrome I304N mutation.
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PLoS Genet,
5,
e1000758.
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J.C.Darnell,
C.E.Fraser,
O.Mostovetsky,
and
R.B.Darnell
(2009).
Discrimination of common and unique RNA-binding activities among Fragile X mental retardation protein paralogs.
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Hum Mol Genet,
18,
3164-3177.
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J.Grillari,
M.Löscher,
M.Denegri,
K.Lee,
K.Fortschegger,
F.Eisenhaber,
P.Ajuh,
A.I.Lamond,
H.Katinger,
and
R.Grillari-Voglauer
(2009).
Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4.
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J Biol Chem,
284,
29193-29204.
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K.Kurimoto,
K.Kuwasako,
A.M.Sandercock,
S.Unzai,
C.V.Robinson,
Y.Muto,
and
S.Yokoyama
(2009).
AU-rich RNA-binding induces changes in the quaternary structure of AUH.
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Proteins,
75,
360-372.
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PDB codes:
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T.Carzaniga,
F.Briani,
S.Zangrossi,
G.Merlino,
P.Marchi,
and
G.Dehò
(2009).
Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited.
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J Bacteriol,
191,
1738-1748.
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C.A.Chénard,
and
S.Richard
(2008).
New implications for the QUAKING RNA binding protein in human disease.
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J Neurosci Res,
86,
233-242.
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K.E.Lukong,
K.W.Chang,
E.W.Khandjian,
and
S.Richard
(2008).
RNA-binding proteins in human genetic disease.
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Trends Genet,
24,
416-425.
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Z.Du,
S.Fenn,
R.Tjhen,
and
T.L.James
(2008).
Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms.
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J Biol Chem,
283,
28757-28766.
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A.Barkan,
L.Klipcan,
O.Ostersetzer,
T.Kawamura,
Y.Asakura,
and
K.P.Watkins
(2007).
The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein.
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RNA,
13,
55-64.
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D.V.Venkitaramani,
and
P.J.Lombroso
(2007).
Molecular basis of genetic neuropsychiatric disorders.
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Child Adolesc Psychiatr Clin N Am,
16,
541-556.
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F.Oberman,
K.Rand,
Y.Maizels,
A.M.Rubinstein,
and
J.K.Yisraeli
(2007).
VICKZ proteins mediate cell migration via their RNA binding activity.
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RNA,
13,
1558-1569.
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M.A.Brykailo,
A.H.Corbett,
and
J.L.Fridovich-Keil
(2007).
Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160.
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Nucleic Acids Res,
35,
1108-1118.
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M.Z.Jia,
J.Ohtsuka,
W.C.Lee,
K.Nagata,
and
M.Tanokura
(2007).
Crystal structure of Dim2p: a preribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 A.
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Proteins,
69,
428-432.
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PDB code:
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P.Banerjee,
S.Nayar,
S.Hebbar,
C.F.Fox,
M.C.Jacobs,
J.H.Park,
J.J.Fernandes,
and
T.C.Dockendorff
(2007).
Substitution of critical isoleucines in the KH domains of Drosophila fragile X protein results in partial loss-of-function phenotypes.
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Genetics,
175,
1241-1250.
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S.Fenn,
Z.Du,
J.K.Lee,
R.Tjhen,
R.M.Stroud,
and
T.L.James
(2007).
Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution.
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Nucleic Acids Res,
35,
2651-2660.
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PDB code:
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W.Wang,
E.van Niekerk,
D.E.Willis,
and
J.L.Twiss
(2007).
RNA transport and localized protein synthesis in neurological disorders and neural repair.
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Dev Neurobiol,
67,
1166-1182.
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N.H.Chmiel,
D.C.Rio,
and
J.A.Doudna
(2006).
Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein.
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RNA,
12,
283-291.
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R.B.Denman
(2006).
mRNPs take shape by CLIPPING and PAIRING.
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Bioessays,
28,
1132-1143.
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H.Nabel-Rosen,
H.Toledano-Katchalski,
G.Volohonsky,
and
T.Volk
(2005).
Cell divisions in the drosophila embryonic mesoderm are repressed via posttranscriptional regulation of string/cdc25 by HOW.
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Curr Biol,
15,
295-302.
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J.C.Darnell,
C.E.Fraser,
O.Mostovetsky,
G.Stefani,
T.A.Jones,
S.R.Eddy,
and
R.B.Darnell
(2005).
Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes.
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Genes Dev,
19,
903-918.
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M.R.Rossi,
J.La Duca,
S.Matsui,
N.J.Nowak,
L.Hawthorn,
and
J.K.Cowell
(2005).
Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme.
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Genes Chromosomes Cancer,
44,
392-404.
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M.Sidiqi,
J.A.Wilce,
C.J.Porter,
A.Barker,
P.J.Leedman,
and
M.C.Wilce
(2005).
Formation of an alphaCP1-KH3 complex with UC-rich RNA.
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Eur Biophys J,
34,
423-429.
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M.Sidiqi,
J.A.Wilce,
J.P.Vivian,
C.J.Porter,
A.Barker,
P.J.Leedman,
and
M.C.Wilce
(2005).
Structure and RNA binding of the third KH domain of poly(C)-binding protein 1.
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Nucleic Acids Res,
33,
1213-1221.
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PDB code:
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P.Gutiérrez,
Y.Li,
M.J.Osborne,
E.Pomerantseva,
Q.Liu,
and
K.Gehring
(2005).
Solution structure of the carbon storage regulator protein CsrA from Escherichia coli.
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J Bacteriol,
187,
3496-3501.
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PDB code:
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K.M.Bedard,
B.L.Walter,
and
B.L.Semler
(2004).
Multimerization of poly(rC) binding protein 2 is required for translation initiation mediated by a viral IRES.
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RNA,
10,
1266-1276.
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K.Musunuru,
and
R.B.Darnell
(2004).
Determination and augmentation of RNA sequence specificity of the Nova K-homology domains.
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Nucleic Acids Res,
32,
4852-4861.
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M.H.Lee,
and
T.Schedl
(2004).
Translation repression by GLD-1 protects its mRNA targets from nonsense-mediated mRNA decay in C. elegans.
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Genes Dev,
18,
1047-1059.
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R.Willemsen,
B.A.Oostra,
G.J.Bassell,
and
J.Dictenberg
(2004).
The fragile X syndrome: from molecular genetics to neurobiology.
|
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Ment Retard Dev Disabil Res Rev,
10,
60-67.
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T.C.Mockler,
X.Yu,
D.Shalitin,
D.Parikh,
T.P.Michael,
J.Liou,
J.Huang,
Z.Smith,
J.M.Alonso,
J.R.Ecker,
J.Chory,
and
C.Lin
(2004).
Regulation of flowering time in Arabidopsis by K homology domain proteins.
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Proc Natl Acad Sci U S A,
101,
12759-12764.
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Y.Ye,
and
A.Godzik
(2004).
Comparative analysis of protein domain organization.
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Genome Res,
14,
343-353.
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Z.Du,
J.Yu,
Y.Chen,
R.Andino,
and
T.L.James
(2004).
Specific recognition of the C-rich strand of human telomeric DNA and the RNA template of human telomerase by the first KH domain of human poly(C)-binding protein-2.
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J Biol Chem,
279,
48126-48134.
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A.Bevilacqua,
M.C.Ceriani,
S.Capaccioli,
and
A.Nicolin
(2003).
Post-transcriptional regulation of gene expression by degradation of messenger RNAs.
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J Cell Physiol,
195,
356-372.
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A.N.Chkheidze,
and
S.A.Liebhaber
(2003).
A novel set of nuclear localization signals determine distributions of the alphaCP RNA-binding proteins.
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Mol Cell Biol,
23,
8405-8415.
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A.Ramos,
D.Hollingworth,
and
A.Pastore
(2003).
The role of a clinically important mutation in the fold and RNA-binding properties of KH motifs.
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RNA,
9,
293-298.
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K.E.Lukong,
and
S.Richard
(2003).
Sam68, the KH domain-containing superSTAR.
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Biochim Biophys Acta,
1653,
73-86.
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K.M.Goolsby,
and
D.J.Shapiro
(2003).
RNAi-mediated depletion of the 15 KH domain protein, vigilin, induces death of dividing and non-dividing human cells but does not initially inhibit protein synthesis.
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Nucleic Acids Res,
31,
5644-5653.
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A.Ramos,
D.Hollingworth,
S.A.Major,
S.Adinolfi,
G.Kelly,
F.W.Muskett,
and
A.Pastore
(2002).
Role of dimerization in KH/RNA complexes: the example of Nova KH3.
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Biochemistry,
41,
4193-4201.
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A.V.Makeyev,
and
S.A.Liebhaber
(2002).
The poly(C)-binding proteins: a multiplicity of functions and a search for mechanisms.
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RNA,
8,
265-278.
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B.L.Walter,
T.B.Parsley,
E.Ehrenfeld,
and
B.L.Semler
(2002).
Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication.
|
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J Virol,
76,
12008-12022.
|
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C.Oubridge,
A.Kuglstatter,
L.Jovine,
and
K.Nagai
(2002).
Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle.
|
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Mol Cell,
9,
1251-1261.
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PDB code:
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G.J.Ostheimer,
A.Barkan,
and
B.W.Matthews
(2002).
Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins.
|
| |
Structure,
10,
1593-1601.
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PDB code:
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J.P.Staley
(2002).
Hanging on to the branch.
|
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Nat Struct Biol,
9,
5-7.
|
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M.Rehbein,
K.Wege,
F.Buck,
M.Schweizer,
D.Richter,
and
S.Kindler
(2002).
Molecular characterization of MARTA1, a protein interacting with the dendritic targeting element of MAP2 mRNAs.
|
| |
J Neurochem,
82,
1039-1046.
|
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R.Campos-Olivas,
J.M.Louis,
D.Clerot,
B.Gronenborn,
and
A.M.Gronenborn
(2002).
The structure of a replication initiator unites diverse aspects of nucleic acid metabolism.
|
| |
Proc Natl Acad Sci U S A,
99,
10310-10315.
|
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PDB codes:
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W.T.O'Donnell,
and
S.T.Warren
(2002).
A decade of molecular studies of fragile X syndrome.
|
| |
Annu Rev Neurosci,
25,
315-338.
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H.Peled-Zehavi,
J.A.Berglund,
M.Rosbash,
and
A.D.Frankel
(2001).
Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex.
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Mol Cell Biol,
21,
5232-5241.
|
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J.M.Pérez-Cañadillas,
and
G.Varani
(2001).
Recent advances in RNA-protein recognition.
|
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Curr Opin Struct Biol,
11,
53-58.
|
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K.Kurimoto,
S.Fukai,
O.Nureki,
Y.Muto,
and
S.Yokoyama
(2001).
Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase.
|
| |
Structure,
9,
1253-1263.
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PDB code:
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K.Musunuru,
and
R.B.Darnell
(2001).
Paraneoplastic neurologic disease antigens: RNA-binding proteins and signaling proteins in neuronal degeneration.
|
| |
Annu Rev Neurosci,
24,
239-262.
|
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M.H.Lee,
and
T.Schedl
(2001).
Identification of in vivo mRNA targets of GLD-1, a maxi-KH motif containing protein required for C. elegans germ cell development.
|
| |
Genes Dev,
15,
2408-2420.
|
|
|
|
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|
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N.V.Grishin
(2001).
KH domain: one motif, two folds.
|
| |
Nucleic Acids Res,
29,
638-643.
|
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|
|
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|
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T.Akiyama,
J.Gohda,
S.Shibata,
Y.Nomura,
S.Azuma,
Y.Ohmori,
S.Sugano,
H.Arai,
T.Yamamoto,
and
J.Inoue
(2001).
Mammalian homologue of E. coli Ras-like GTPase (ERA) is a possible apoptosis regulator with RNA binding activity.
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Genes Cells,
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Molecular characterization of global regulatory RNA species that control pathogenicity factors in Erwinia amylovora and Erwinia herbicola pv. gypsophilae.
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Structural basis for recognition of the intron branch site RNA by splicing factor 1.
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Science,
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PDB code:
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Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
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Cell,
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PDB code:
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H.Kondoh,
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Mis3 with a conserved RNA binding motif is essential for ribosome biogenesis and implicated in the start of cell growth and S phase checkpoint.
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Biochemistry,
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Structure,
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PDB codes:
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M.Huynen,
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PDB code:
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The N-terminal K homology domain of the poly(rC)-binding protein is a major determinant for binding to the poliovirus 5'-untranslated region and acts as an inhibitor of viral translation.
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J Biol Chem,
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Structure,
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PDB codes:
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H.Nabel-Rosen,
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The balance between two isoforms of the Drosophila RNA-binding protein how controls tendon cell differentiation.
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Mol Cell,
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RNA,
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Dissecting FMR1, the protein responsible for fragile X syndrome, in its structural and functional domains.
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RNA,
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T.Chen,
F.M.Boisvert,
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A role for the GSG domain in localizing Sam68 to novel nuclear structures in cancer cell lines.
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Mol Biol Cell,
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X.Chen,
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Crystal structure of ERA: a GTPase-dependent cell cycle regulator containing an RNA binding motif.
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Proc Natl Acad Sci U S A,
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PDB code:
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Premature translation of oskar in oocytes lacking the RNA-binding protein bicaudal-C.
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Mol Cell Biol,
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In vitro genetic analysis of the RNA binding site of vigilin, a multi-KH-domain protein.
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Mol Cell Biol,
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J.A.Berglund,
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The KH domain of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence.
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RNA,
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RNA,
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Structure and mechanism in transcriptional antitermination by the bacteriophage lambda N protein.
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Cold Spring Harb Symp Quant Biol,
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J.Mezquita,
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Four isoforms of the signal-transduction and RNA-binding protein QKI expressed during chicken spermatogenesis.
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Mol Reprod Dev,
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A highly conserved RNA-binding protein for cytoplasmic mRNA localization in vertebrates.
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Curr Biol,
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Nat Struct Biol,
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The identification of two Drosophila K homology domain proteins. Kep1 and SAM are members of the Sam68 family of GSG domain proteins.
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J Biol Chem,
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Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein.
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EMBO J,
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PDB code:
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R.B.Russell,
and
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Protein fold irregularities that hinder sequence analysis.
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Curr Opin Struct Biol,
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QKI expression is regulated during neuron-glial cell fate decisions.
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Mol Cell Biol,
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Purified recombinant Fmrp exhibits selective RNA binding as an intrinsic property of the fragile X mental retardation protein.
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J Biol Chem,
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The KH domain protein encoded by quaking functions as a dimer and is essential for notochord development in Xenopus embryos.
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Genes Dev,
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STAR, a gene family involved in signal transduction and activation of RNA.
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Trends Genet,
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The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14.
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EMBO J,
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PDB code:
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G.Musco,
A.Kharrat,
G.Stier,
F.Fraternali,
T.J.Gibson,
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The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome.
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Nat Struct Biol,
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PDB code:
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H.Siomi,
and
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RNA-binding proteins as regulators of gene expression.
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Curr Opin Genet Dev,
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S.Aymerich,
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Crystal structure of a new RNA-binding domain from the antiterminator protein SacY of Bacillus subtilis.
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EMBO J,
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Fragile X mental retardation protein is translated near synapses in response to neurotransmitter activation.
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Proc Natl Acad Sci U S A,
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Multiple RRMs contribute to RNA binding specificity and affinity for polypyrimidine tract binding protein.
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Biochemistry,
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The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.
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Cell,
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Cell,
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PDB code:
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N.Abovich,
and
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Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals.
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Cell,
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Organelle-specific targeting of protein kinase AII (PKAII). Molecular and in situ characterization of murine A kinase anchor proteins that recruit regulatory subunits of PKAII to the cytoplasmic surface of mitochondria.
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J Biol Chem,
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Specificity and determinants of Sam68 RNA binding. Implications for the biological function of K homology domains.
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Mol Cell Biol,
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Mol Cell Biol,
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FMRP associates with polyribosomes as an mRNP, and the I304N mutation of severe fragile X syndrome abolishes this association.
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MEX-3 is a KH domain protein that regulates blastomere identity in early C. elegans embryos.
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Cell,
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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
codes are
shown on the right.
|
|
Links
