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PDBsum entry 1wr0
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Protein transport
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PDB id
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1wr0
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Contents |
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* Residue conservation analysis
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PDB id:
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Protein transport
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Title:
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Structural characterization of the mit domain from human vps4b
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Structure:
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Skd1 protein. Chain: a. Fragment: mit domain. Synonym: vacuolar sorting protein 4b. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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NMR struc:
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20 models
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Authors:
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H.Takasu,J.G.Jee,A.Ohno,N.Goda,K.Fujiwara,H.Tochio,M.Shirakawa, H.Hiroaki,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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H.Takasu
et al.
(2005).
Structural characterization of the MIT domain from human Vps4b.
Biochem Biophys Res Commun,
334,
460-465.
PubMed id:
DOI:
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Date:
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07-Oct-04
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Release date:
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02-Aug-05
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PROCHECK
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Headers
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References
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O75351
(VPS4B_HUMAN) -
Vacuolar protein sorting-associated protein 4B from Homo sapiens
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Seq:
Struc:
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444 a.a.
81 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.6.4.6
- vesicle-fusing ATPase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
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+
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H2O
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=
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ADP
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+
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phosphate
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+
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H(+)
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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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Biochem Biophys Res Commun
334:460-465
(2005)
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PubMed id:
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Structural characterization of the MIT domain from human Vps4b.
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H.Takasu,
J.G.Jee,
A.Ohno,
N.Goda,
K.Fujiwara,
H.Tochio,
M.Shirakawa,
H.Hiroaki.
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ABSTRACT
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The microtubule interacting and trafficking (MIT) domain is a small protein
module of unknown function that is conserved in proteins of diverse function,
such as Vps4, sorting nexin 15 (SNX15), and spastin. One non-synonymous single
nucleotide polymorphism was reported, which results in a Ile58-to-Met (I58M)
substitution in hVps4b. Here, we have determined the solution structure of the
MIT domain isolated from the NH(2)-terminus of human Vps4b, an AAA-ATPase
involved in multivesicular body formation. The MIT domain adopts an
'up-and-down' three-helix bundle. Comparison with the sequences of other MIT
domains clearly shows that the residues involved in inter-helical contacts are
well conserved. The Ile58-to-Met substitution resulted a substantial thermal
instability. In addition, we found a shallow crevice between helices A and C
that may serve as a protein-binding site. We propose that the MIT domain serves
as a putative adaptor domain for the ESCRT-III complex involved in endosomal
trafficking.
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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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M.Agromayor,
J.G.Carlton,
J.P.Phelan,
D.R.Matthews,
L.M.Carlin,
S.Ameer-Beg,
K.Bowers,
and
J.Martin-Serrano
(2009).
Essential role of hIST1 in cytokinesis.
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Mol Biol Cell,
20,
1374-1387.
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C.Kieffer,
J.J.Skalicky,
E.Morita,
I.De Domenico,
D.M.Ward,
J.Kaplan,
and
W.I.Sundquist
(2008).
Two distinct modes of ESCRT-III recognition are required for VPS4 functions in lysosomal protein targeting and HIV-1 budding.
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Dev Cell,
15,
62-73.
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PDB code:
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C.Yorikawa,
E.Takaya,
Y.Osako,
R.Tanaka,
Y.Terasawa,
T.Hamakubo,
Y.Mochizuki,
H.Iwanari,
T.Kodama,
T.Maeda,
K.Hitomi,
H.Shibata,
and
M.Maki
(2008).
Human calpain 7/PalBH associates with a subset of ESCRT-III-related proteins in its N-terminal region and partly localizes to endocytic membrane compartments.
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J Biochem,
143,
731-745.
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J.Xiao,
H.Xia,
J.Zhou,
I.F.Azmi,
B.A.Davies,
D.J.Katzmann,
and
Z.Xu
(2008).
Structural basis of Vta1 function in the multivesicular body sorting pathway.
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Dev Cell,
14,
37-49.
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PDB codes:
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P.R.Vajjhala,
C.H.Nguyen,
M.J.Landsberg,
C.Kistler,
A.L.Gan,
G.F.King,
B.Hankamer,
and
A.L.Munn
(2008).
The Vps4 C-terminal helix is a critical determinant for assembly and ATPase activity and has elements conserved in other members of the meiotic clade of AAA ATPases.
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FEBS J,
275,
1427-1449.
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M.D.Stuchell-Brereton,
J.J.Skalicky,
C.Kieffer,
M.A.Karren,
S.Ghaffarian,
and
W.I.Sundquist
(2007).
ESCRT-III recognition by VPS4 ATPases.
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Nature,
449,
740-744.
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PDB codes:
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N.Iwaya,
N.Goda,
S.Unzai,
K.Fujiwara,
T.Tanaka,
K.Tomii,
H.Tochio,
M.Shirakawa,
and
H.Hiroaki
(2007).
Fine-tuning of protein domain boundary by minimizing potential coiled coil regions.
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J Biomol NMR,
37,
53-63.
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P.R.Vajjhala,
E.Catchpoole,
C.H.Nguyen,
C.Kistler,
and
A.L.Munn
(2007).
Vps4 regulates a subset of protein interactions at the multivesicular endosome.
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FEBS J,
274,
1894-1907.
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S.Salinas,
R.E.Carazo-Salas,
C.Proukakis,
G.Schiavo,
and
T.T.Warner
(2007).
Spastin and microtubules: Functions in health and disease.
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J Neurosci Res,
85,
2778-2782.
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S.Shim,
L.A.Kimpler,
and
P.I.Hanson
(2007).
Structure/function analysis of four core ESCRT-III proteins reveals common regulatory role for extreme C-terminal domain.
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Traffic,
8,
1068-1079.
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T.Obita,
S.Saksena,
S.Ghazi-Tabatabai,
D.J.Gill,
O.Perisic,
S.D.Emr,
and
R.L.Williams
(2007).
Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4.
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Nature,
449,
735-739.
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PDB codes:
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K.Shiozawa,
N.Goda,
T.Shimizu,
K.Mizuguchi,
N.Kondo,
N.Shimozawa,
M.Shirakawa,
and
H.Hiroaki
(2006).
The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97.
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FEBS J,
273,
4959-4971.
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M.R.Russell,
D.P.Nickerson,
and
G.Odorizzi
(2006).
Molecular mechanisms of late endosome morphology, identity and sorting.
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Curr Opin Cell Biol,
18,
422-428.
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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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Links
