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PDBsum entry 1iym
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DNA binding protein
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PDB id
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1iym
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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High precision nmr structure and function of the ring-H2 finger domain of el5, A rice protein whose expression is increased upon exposure to pathogen-Derived oligosaccharides.
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Authors
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S.Katoh,
C.Hong,
Y.Tsunoda,
K.Murata,
R.Takai,
E.Minami,
T.Yamazaki,
E.Katoh.
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Ref.
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J Biol Chem, 2003,
278,
15341-15348.
[DOI no: ]
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PubMed id
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Abstract
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EL5, a RING-H2 finger protein, is rapidly induced by
N-acetylchitooligosaccharides in rice cell. We expressed the EL5 RING-H2 finger
domain in Escherichia coli and determined its structure in solution by NMR
spectroscopy. The EL5 RING-H2 finger domain consists of two-stranded beta-sheets
(beta1, Ala(147)-Phe(149); beta2, Gly(156)-His(158)), one alpha-helix
(Cys(161)-Leu(166)), and two large N- and C-terminal loops. It is stabilized by
two tetrahedrally coordinated zinc ions. This structure is similar to that of
other RING finger domains of proteins of known function. From structural
analogies, we inferred that the EL5 RING-H2 finger is a binding domain for
ubiquitin-conjugating enzyme (E2). The binding site is probably formed by
solvent-exposed hydrophobic residues of the N- and C-terminal loops and the
alpha-helix. We demonstrated that the fusion protein with EL5-(96-181) and
maltose-binding protein (MBP) was polyubiquitinated by incubation with
ubiquitin, ubiquitin-activating enzyme (E1), and a rice E2 protein, OsUBC5b.
This supported the idea that the EL5 RING finger domain is essential for
ubiquitin-ligase activity of EL5. By NMR titration experiments, we identified
residues that are critical for the interaction between the EL5 RING-H2 finger
and OsUBC5b. We conclude that the RING-H2 finger domain of EL5 is the E2 binding
site of EL5.
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Figure 2.
Fig. 2. a, best-fit superposition of the backbone (N, C
 , and C')
atoms of the final 15 structures of the RING-H2 finger domain of
EL5. The structures are superimposed on the energy-minimized
average structure using the backbone coordinates of residues
132-178. b, ribbon diagram of the energy-minimized average
structure of the RING-H2 finger domain of EL5.
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Figure 3.
Fig. 3. a, comparison of the free RING finger domain of
EL5 with the E2-bound form of c-Cbl and the dimerization domain
of RAG1. The additional -helices at
the N and C termini of RAG1 are shown in yellow. b, surface
potential representations of these domains. Positively charged
areas are blue, and negatively charged areas are red. The
hydrophobic grooves in c-Cbl and EL5 are indicated by arrows.
The atomic coordinates for c-Cbl and RAG1 were downloaded from
the Protein Data Bank at Brookhaven National Laboratory
(accession numbers: 1FBV and 1RMD, respectively).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
15341-15348)
copyright 2003.
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