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PDBsum entry 2pyh
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Contents |
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* Residue conservation analysis
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PDB id:
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Isomerase
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Title:
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Azotobacter vinelandii mannuronan c-5 epimerase alge4 a-module complexed with mannuronan trisaccharide
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Structure:
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Poly(beta-d-mannuronate) c5 epimerase 4. Chain: a, b. Fragment: a-module. Synonym: mannuronan epimerase 4. Engineered: yes
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Source:
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Azotobacter vinelandii. Organism_taxid: 354. Gene: alge4. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.70Å
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R-factor:
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0.233
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R-free:
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0.279
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Authors:
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H.J.Rozeboom,T.M.Bjerkan,K.H.Kalk,H.Ertesvag,S.Holtan,F.L.Aachman, S.Valla,B.W.Dijkstra
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Key ref:
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H.J.Rozeboom
et al.
(2008).
Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.
J Biol Chem,
283,
23819-23828.
PubMed id:
DOI:
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Date:
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16-May-07
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Release date:
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27-May-08
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PROCHECK
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Headers
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References
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Q44493
(ALGE4_AZOVI) -
Mannuronan C5-epimerase AlgE4 from Azotobacter vinelandii
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Seq:
Struc:
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553 a.a.
376 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.5.1.3.37
- mannuronan 5-epimerase.
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Reaction:
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[(1->4)-beta-D-mannuronosyl](n) = [alginate](n)
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DOI no:
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J Biol Chem
283:23819-23828
(2008)
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PubMed id:
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Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.
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H.J.Rozeboom,
T.M.Bjerkan,
K.H.Kalk,
H.Ertesvåg,
S.Holtan,
F.L.Aachmann,
S.Valla,
B.W.Dijkstra.
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ABSTRACT
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Alginate is a family of linear copolymers of (1-->4)-linked beta-d-mannuronic
acid and its C-5 epimer alpha-l-guluronic acid. The polymer is first produced as
polymannuronic acid and the guluronic acid residues are then introduced at the
polymer level by mannuronan C-5-epimerases. The structure of the catalytic
A-module of the Azotobacter vinelandii mannuronan C-5-epimerase AlgE4 has been
determined by x-ray crystallography at 2.1-A resolution. AlgE4A folds into a
right-handed parallel beta-helix structure originally found in pectate lyase C
and subsequently in several polysaccharide lyases and hydrolases. The beta-helix
is composed of four parallel beta-sheets, comprising 12 complete turns, and has
an amphipathic alpha-helix near the N terminus. The catalytic site is positioned
in a positively charged cleft formed by loops extending from the surface
encompassing Asp(152), an amino acid previously shown to be important for the
reaction. Site-directed mutagenesis further implicates Tyr(149), His(154), and
Asp(178) as being essential for activity. Tyr(149) probably acts as the proton
acceptor, whereas His(154) is the proton donor in the epimerization reaction.
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Selected figure(s)
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Figure 5.
FIGURE 5. Superimposition of the active site residues of
ALY-1 in green (His^119, Gln^117, Arg^72, and Tyr^195), A1-III
(His^192, Asn^191, Arg^239, Tyr^246, and trisaccharide) in
lilac, and AlgE4A (His^154, Asp^152, Lys^117, and Tyr^149 and
trisaccharide) in CPK colors. The image was constructed in PyMOL
(52).
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Figure 7.
FIGURE 7. Proposed catalytic mechanism of AlgE4. A and B,
the alginate polymer enters the catalytic site. B and C, the
carboxylate moiety of the mannuronic acid in subsite +1 is
protonated, enabling it to form a hydrogen bond with Asp^152
(and/or 178), which stabilizes the substrate-enzyme complex. C,
upon deprotonation of Tyr^149 (via Arg^195) the alkoxide ion
group extracts H-5 from the re-face of the mannuronic acid in
subsite +1. C and D, a double bond is formed, which makes the
conformation of the +1 mannuronic acid partially planar. D, the
protonated His^154 performs a nucleophilic attack on the C-5
atom of the +1 sugar from the si-face with the concomitant flip
of the +1 sugar ring into the ^1C[4] chair conformation of
guluronic acid. D and E, the carboxylic acid moiety on sugar +1
is deprotonated. E and F, the epimerized sugar leaves the active
site and His^154 is protonated again. F, the epimerase is ready
to perform a new reaction.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
23819-23828)
copyright 2008.
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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.Raedts,
S.W.Kengen,
and
J.van der Oost
(2011).
Occurrence of L-iduronic acid and putative D-glucuronyl C5-epimerases in prokaryotes.
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Glycoconj J,
28,
57-66.
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E.Buchinger,
F.L.Aachmann,
A.S.Aranko,
S.Valla,
G.Skjåk-Braek,
H.Iwaï,
and
R.Wimmer
(2010).
Use of protein trans-splicing to produce active and segmentally (2)H, (15)N labeled mannuronan C5-epimerase AlgE4.
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Protein Sci,
19,
1534-1543.
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T.Ishida,
S.Fushinobu,
R.Kawai,
M.Kitaoka,
K.Igarashi,
and
M.Samejima
(2009).
Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium.
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J Biol Chem,
284,
10100-10109.
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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
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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.
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