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PDBsum entry 1fp0
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Transcription
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PDB id
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1fp0
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.3.2.27
- RING-type E3 ubiquitin transferase.
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Reaction:
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S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6- ubiquitinyl-[acceptor protein]-L-lysine
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DOI no:
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EMBO J
20:165-177
(2001)
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PubMed id:
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Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.
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A.D.Capili,
D.C.Schultz,
F.J.RauscherIII,
K.L.Borden.
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ABSTRACT
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Plant homeodomain (PHD) domains are found in >400 eukaryotic proteins, many of
which are transcriptional regulators. Naturally occurring point mutations or
deletions of this domain contribute to a variety of human diseases, including
ATRX syndrome, myeloid leukemias and autoimmune dysfunction. Here we report the
first structural characterization of a PHD domain. Our studies reveal that the
PHD domain from KAP-1 corepressor binds zinc in a cross-brace topology between
anti-parallel ss-strands reminiscent of RING (really interesting new gene)
domains. Using a mutational analysis, we define the structural features required
for transcriptional repression by KAP-1 and explain naturally occurring,
disease-causing mutations in PHD domains of other proteins. From a comparison of
this PHD structure with previously reported RING and LIM (Lin11/Isl-1/Mec-3)
structures, we infer sequence determinants that allow discrimination among PHD,
RING and LIM motifs.
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Selected figure(s)
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Figure 4.
Figure 4 Comparison of the KAP-1 PHD, PML RING, IEEHV RING and
RAG1 RING. Superposition of KAP-1 PHD (with blue  -strands,
aa 627 -652) and PML RING (magenta -strands,
aa 56 -81) (A) and RAG1 RING (yellow -strands,
aa 292 -317) (B) from the first metal ligand to the sixth metal
ligand. The white spheres represent zinc atoms with the upper
zinc atom being site I. The orientation of KAP-1 PHD is the same
in both panels. (C) Superposition of zinc-binding site I for
KAP-1 (627 -632, 647 -652), PML (56 -71, 76 -81), IEEHV (7 -12,
28 -33) and RAG1 (292 -297, 312 -317). The metal ligands are
colored according to protein: KAP-1 in blue, PML in magenta,
IEEHV in green and RAG1 in yellow. (D) Superposition of the
conserved hydrophobic core residues N-terminal to metal ligand 5
and C-terminal to metal ligand 6 (L76 and L81 in PML, F28 and
I33 in IEEHV, and F312, I317, F647 and H652 in PHD). The
side-chains are colored as in (C). The core residues from PHD
are noted for clarity. The conserved tryptophan within the PHD
family (W664 in KAP-1) is seen here inserting between the other
core residues, repositioning the core.
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Figure 5.
Figure 5 Amino acid sequence alignment of the PHD, RING and LIM
families. Site I metal ligands are colored in magenta and site
II metal ligands in blue. Conserved hydrophobic core residues
are colored in yellow. DDBJ/EMBL/GenBank accession Nos and PDB
codes: KAP-1 (U78773), TIF1  (AAD17258),
Mi2 (Q14839),
ATRX (P46100), DNMt3A (BAA95556), ING1 (AAG02578), YNJ7_YEAST
(P50947), RBB2_HUMAN (P29375), YM42_YEAST (Q03214), YMW5_YEAST
(Q04779), YA27_SCHPO (Q09698), YAC5_SCHPO (Q09819), AIRE_HUMAN
(O43918), CHD4_HUMAN (Q14839), X169_HUMAN (CAA89909), HT31_ARATH
(Q04996), PRH_ARATH (P48785), CHD3_CAEEL (Q22516), CHD3_HUMAN
(Q12873), YJ89_YEAST (P47156), FALZ_HUMAN (Q12830), YANC_SCHPO
(Q10077), YGN1_YEAST (P53127), YAJ8_SCHPO (Q09908), AF17_HUMAN
(Q09908), YGN1_YEAST (P53127), HRX_HUMAN (Q03164), PML (1bor),
IEEHV (1chc), RAG1 (1RMD), BRCA1 (A58881), BARD1 (NP_00456),
c-Cbl (P22681), MDM2 (CAA41684), MDMX (O15151), MAT (S60157), Z
(P18541), Mel-18 (P35227), Crp1LIM1 and LIM2 (1B8T), CRIPrat
(1IML), Lin-11 (CAA38240), ISL-1 (CAA3749), MEC-3 (S28390),
LMX-1 (B46233).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2001,
20,
165-177)
copyright 2001.
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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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A.H.Aguissa-Touré,
R.P.Wong,
and
G.Li
(2011).
The ING family tumor suppressors: from structure to function.
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Cell Mol Life Sci,
68,
45-54.
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K.L.Yap,
and
M.M.Zhou
(2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
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Crit Rev Biochem Mol Biol,
45,
488-505.
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M.Mitra,
and
A.Melis
(2010).
Genetic and biochemical analysis of the TLA1 gene in Chlamydomonas reinhardtii.
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Planta,
231,
729-740.
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S.Sue Ng,
T.Mahmoudi,
V.S.Li,
P.Hatzis,
P.J.Boersema,
S.Mohammed,
A.J.Heck,
and
H.Clevers
(2010).
MAP3K1 functionally interacts with Axin1 in the canonical Wnt signalling pathway.
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Biol Chem,
391,
171-180.
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T.C.Miller,
T.J.Rutherford,
C.M.Johnson,
M.Fiedler,
and
M.Bienz
(2010).
Allosteric remodelling of the histone H3 binding pocket in the Pygo2 PHD finger triggered by its binding to the B9L/BCL9 co-factor.
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J Mol Biol,
401,
969-984.
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PDB code:
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M.de la Paz Sanchez,
and
C.Gutierrez
(2009).
Arabidopsis ORC1 is a PHD-containing H3K4me3 effector that regulates transcription.
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Proc Natl Acad Sci U S A,
106,
2065-2070.
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S.Chakravarty,
L.Zeng,
and
M.M.Zhou
(2009).
Structure and site-specific recognition of histone H3 by the PHD finger of human autoimmune regulator.
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Structure,
17,
670-679.
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PDB code:
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W.Wei,
J.Huang,
Y.J.Hao,
H.F.Zou,
H.W.Wang,
J.Y.Zhao,
X.Y.Liu,
W.K.Zhang,
B.Ma,
J.S.Zhang,
and
S.Y.Chen
(2009).
Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants.
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PLoS One,
4,
e7209.
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Y.Nakajima,
H.Okamoto,
and
T.Kubo
(2009).
Expression cloning of Xenopus zygote arrest 2 (Xzar2) as a novel epidermalization-promoting factor in early embryos of Xenopus laevis.
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Genes Cells,
14,
583-595.
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D.Ju,
X.Wang,
H.Xu,
and
Y.Xie
(2008).
Genome-wide analysis identifies MYND-domain protein Mub1 as an essential factor for Rpn4 ubiquitylation.
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Mol Cell Biol,
28,
1404-1412.
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L.Zeng,
K.L.Yap,
A.V.Ivanov,
X.Wang,
S.Mujtaba,
O.Plotnikova,
F.J.Rauscher,
and
M.M.Zhou
(2008).
Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing.
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Nat Struct Mol Biol,
15,
626-633.
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PDB code:
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P.V.Peña,
R.A.Hom,
T.Hung,
H.Lin,
A.J.Kuo,
R.P.Wong,
O.M.Subach,
K.S.Champagne,
R.Zhao,
V.V.Verkhusha,
G.Li,
O.Gozani,
and
T.G.Kutateladze
(2008).
Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
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J Mol Biol,
380,
303-312.
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PDB code:
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A.Argentaro,
J.C.Yang,
L.Chapman,
M.S.Kowalczyk,
R.J.Gibbons,
D.R.Higgs,
D.Neuhaus,
and
D.Rhodes
(2007).
Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX.
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Proc Natl Acad Sci U S A,
104,
11939-11944.
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PDB codes:
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A.Barrett,
S.Santangelo,
K.Tan,
S.Catchpole,
K.Roberts,
B.Spencer-Dene,
D.Hall,
A.Scibetta,
J.Burchell,
E.Verdin,
P.Freemont,
and
J.Taylor-Papadimitriou
(2007).
Breast cancer associated transcriptional repressor PLU-1/JARID1B interacts directly with histone deacetylases.
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Int J Cancer,
121,
265-275.
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A.V.Ivanov,
H.Peng,
V.Yurchenko,
K.L.Yap,
D.G.Negorev,
D.C.Schultz,
E.Psulkowski,
W.J.Fredericks,
D.E.White,
G.G.Maul,
M.J.Sadofsky,
M.M.Zhou,
and
F.J.Rauscher
(2007).
PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing.
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Mol Cell,
28,
823-837.
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B.E.Dul,
and
N.C.Walworth
(2007).
The plant homeodomain fingers of fission yeast Msc1 exhibit E3 ubiquitin ligase activity.
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J Biol Chem,
282,
18397-18406.
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E.Leithe,
and
E.Rivedal
(2007).
Ubiquitination of gap junction proteins.
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J Membr Biol,
217,
43-51.
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S.Ahmed,
B.Dul,
X.Qiu,
and
N.C.Walworth
(2007).
Msc1 acts through histone H2A.Z to promote chromosome stability in Schizosaccharomyces pombe.
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Genetics,
177,
1487-1497.
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T.Tanaka,
M.J.Grusby,
and
T.Kaisho
(2007).
PDLIM2-mediated termination of transcription factor NF-kappaB activation by intranuclear sequestration and degradation of the p65 subunit.
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Nat Immunol,
8,
584-591.
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X.H.Mascle,
D.Germain-Desprez,
P.Huynh,
P.Estephan,
and
M.Aubry
(2007).
Sumoylation of the transcriptional intermediary factor 1beta (TIF1beta), the Co-repressor of the KRAB Multifinger proteins, is required for its transcriptional activity and is modulated by the KRAB domain.
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J Biol Chem,
282,
10190-10202.
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Y.Xia,
J.Wang,
S.Xu,
G.L.Johnson,
T.Hunter,
and
Z.Lu
(2007).
MEKK1 mediates the ubiquitination and degradation of c-Jun in response to osmotic stress.
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Mol Cell Biol,
27,
510-517.
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C.C.García,
M.Djavani,
I.Topisirovic,
K.L.Borden,
M.S.Salvato,
and
E.B.Damonte
(2006).
Arenavirus Z protein as an antiviral target: virus inactivation and protein oligomerization by zinc finger-reactive compounds.
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J Gen Virol,
87,
1217-1228.
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H.Li,
S.Ilin,
W.Wang,
E.M.Duncan,
J.Wysocka,
C.D.Allis,
and
D.J.Patel
(2006).
Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
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Nature,
442,
91-95.
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PDB codes:
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M.Bienz
(2006).
The PHD finger, a nuclear protein-interaction domain.
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Trends Biochem Sci,
31,
35-40.
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S.P.Sripathy,
J.Stevens,
and
D.C.Schultz
(2006).
The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression.
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Mol Cell Biol,
26,
8623-8638.
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G.Mohrmann,
J.G.Hengstler,
T.G.Hofmann,
S.U.Endele,
B.Lee,
C.Stelzer,
B.Zabel,
J.Brieger,
D.Hasenclever,
B.Tanner,
J.Sagemueller,
J.Sehouli,
H.Will,
and
A.Winterpacht
(2005).
SPOC1, a novel PHD-finger protein: association with residual disease and survival in ovarian cancer.
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Int J Cancer,
116,
547-554.
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J.Hennig,
L.Ottosson,
C.Andrésen,
L.Horvath,
V.K.Kuchroo,
K.Broo,
M.Wahren-Herlenius,
and
M.Sunnerhagen
(2005).
Structural organization and Zn2+-dependent subdomain interactions involving autoantigenic epitopes in the Ring-B-box-coiled-coil (RBCC) region of Ro52.
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J Biol Chem,
280,
33250-33261.
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J.Villaseñor,
C.Benoist,
and
D.Mathis
(2005).
AIRE and APECED: molecular insights into an autoimmune disease.
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Immunol Rev,
204,
156-164.
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K.Tatematsu,
N.Yoshimoto,
T.Koyanagi,
C.Tokunaga,
T.Tachibana,
Y.Yoneda,
M.Yoshida,
T.Okajima,
K.Tanizawa,
and
S.Kuroda
(2005).
Nuclear-cytoplasmic shuttling of a RING-IBR protein RBCK1 and its functional interaction with nuclear body proteins.
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J Biol Chem,
280,
22937-22944.
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M.J.Bottomley,
G.Stier,
D.Pennacchini,
G.Legube,
B.Simon,
A.Akhtar,
M.Sattler,
and
G.Musco
(2005).
NMR structure of the first PHD finger of autoimmune regulator protein (AIRE1). Insights into autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) disease.
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J Biol Chem,
280,
11505-11512.
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PDB code:
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M.Pérez-Alegre,
A.Dubus,
and
E.Fernández
(2005).
REM1, a new type of long terminal repeat retrotransposon in Chlamydomonas reinhardtii.
|
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Mol Cell Biol,
25,
10628-10638.
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S.K.Elkin,
D.Ivanov,
M.Ewalt,
C.G.Ferguson,
S.G.Hyberts,
Z.Y.Sun,
G.D.Prestwich,
J.Yuan,
G.Wagner,
M.A.Oettinger,
and
O.P.Gozani
(2005).
A PHD finger motif in the C terminus of RAG2 modulates recombination activity.
|
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J Biol Chem,
280,
28701-28710.
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PDB codes:
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T.Tanaka,
M.A.Soriano,
and
M.J.Grusby
(2005).
SLIM is a nuclear ubiquitin E3 ligase that negatively regulates STAT signaling.
|
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Immunity,
22,
729-736.
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T.Tasaki,
L.C.Mulder,
A.Iwamatsu,
M.J.Lee,
I.V.Davydov,
A.Varshavsky,
M.Muesing,
and
Y.T.Kwon
(2005).
A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons.
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Mol Cell Biol,
25,
7120-7136.
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X.Shi,
and
O.Gozani
(2005).
The fellowships of the INGs.
|
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J Cell Biochem,
96,
1127-1136.
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A.Eberharter,
I.Vetter,
R.Ferreira,
and
P.B.Becker
(2004).
ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD-histone contacts.
|
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EMBO J,
23,
4029-4039.
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C.Betz,
G.Schlenstedt,
and
S.M.Bailer
(2004).
Asr1p, a novel yeast ring/PHD finger protein, signals alcohol stress to the nucleus.
|
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J Biol Chem,
279,
28174-28181.
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C.M.Horvath
(2004).
Weapons of STAT destruction. Interferon evasion by paramyxovirus V protein.
|
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Eur J Biochem,
271,
4621-4628.
|
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D.R.Jones,
and
N.Divecha
(2004).
Linking lipids to chromatin.
|
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Curr Opin Genet Dev,
14,
196-202.
|
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D.Uchida,
S.Hatakeyama,
A.Matsushima,
H.Han,
S.Ishido,
H.Hotta,
J.Kudoh,
N.Shimizu,
V.Doucas,
K.I.Nakayama,
N.Kuroda,
and
M.Matsumoto
(2004).
AIRE functions as an E3 ubiquitin ligase.
|
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J Exp Med,
199,
167-172.
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E.W.Hewitt,
and
G.E.Dugan
(2004).
Virus subversion of protective immunity.
|
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Curr Allergy Asthma Rep,
4,
365-370.
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F.M.Townsley,
B.Thompson,
and
M.Bienz
(2004).
Pygopus residues required for its binding to Legless are critical for transcription and development.
|
| |
J Biol Chem,
279,
5177-5183.
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H.Akiyoshi,
S.Hatakeyama,
J.Pitkänen,
Y.Mouri,
V.Doucas,
J.Kudoh,
K.Tsurugaya,
D.Uchida,
A.Matsushima,
K.Oshikawa,
K.I.Nakayama,
N.Shimizu,
P.Peterson,
and
M.Matsumoto
(2004).
Subcellular expression of autoimmune regulator is organized in a spatiotemporal manner.
|
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J Biol Chem,
279,
33984-33991.
|
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M.J.Bottomley
(2004).
Structures of protein domains that create or recognize histone modifications.
|
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EMBO Rep,
5,
464-469.
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P.De,
and
K.K.Rodgers
(2004).
Putting the pieces together: identification and characterization of structural domains in the V(D)J recombination protein RAG1.
|
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Immunol Rev,
200,
70-82.
|
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R.B.Dodd,
M.D.Allen,
S.E.Brown,
C.M.Sanderson,
L.M.Duncan,
P.J.Lehner,
M.Bycroft,
and
R.J.Read
(2004).
Solution structure of the Kaposi's sarcoma-associated herpesvirus K3 N-terminal domain reveals a Novel E2-binding C4HC3-type RING domain.
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J Biol Chem,
279,
53840-53847.
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PDB code:
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S.Puig,
M.Lau,
and
D.J.Thiele
(2004).
Cti6 is an Rpd3-Sin3 histone deacetylase-associated protein required for growth under iron-limiting conditions in Saccharomyces cerevisiae.
|
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J Biol Chem,
279,
30298-30306.
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W.Bi,
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Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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|
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