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PDBsum entry 1rwc
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* Residue conservation analysis
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Enzyme class:
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E.C.4.2.2.5
- chondroitin Ac lyase.
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Reaction:
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Eliminative degradation of polysaccharides containing 1,4-beta-D- hexosaminyl and 1,3-beta-D-glucuronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups.
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DOI no:
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J Mol Biol
337:367-386
(2004)
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PubMed id:
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High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism.
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V.V.Lunin,
Y.Li,
R.J.Linhardt,
H.Miyazono,
M.Kyogashima,
T.Kaneko,
A.W.Bell,
M.Cygler.
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ABSTRACT
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Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading
enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens
(ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate
but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of
cleaving hyaluronan. We have determined the three-dimensional crystal structure
of ArthroAC in its native form as well as in complex with its substrates
(chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan
tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence
of ArthroAC has not been previously determined but it was possible to determine
the amino acid sequence of this enzyme from the high-resolution electron density
maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were
obtained by soaking the substrate into the crystals for varying lengths of time
(30 seconds to ten hours) and flash-cooling the crystals. The electron density
map for crystals soaked in the substrate for as short as 30 seconds showed the
substrate clearly and indicated that the ring of central glucuronic acid assumes
a distorted boat conformation. This structure strongly supports the lytic
mechanism where Tyr242 acts as a general base that abstracts the proton from the
C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on
the glucuronate acidic group. Comparison of this structure with that of
chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an
explanation for the exolytic and endolytic mode of action of ArthroAC and
FlavoAC, respectively.
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Selected figure(s)
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Figure 4.
Figure 4. (a) Stereo view of the superposition of the C^a
traces of ArthroAC (blue) and SpHL (1EGU) (red); (b) overlay of
oligosaccharide substrates from ArthroAC (blue), FlavoAC(Y234F)
(1HMW, magenta) and SpHL(Y408F) (1LXK, green) based on the
superposition of the backbone of active site Asn, His, Tyr (Phe)
and Arg residues. The Figure was prepared with programs
sPDBv[51.] and POV-Ray(TM) (http://www.povray.org/).
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Figure 6.
Figure 6. Stereo view of the conformation of the 460-469
loop in native and complexed ArthroAC (blue) and in ArthroAC-Hg
(magenta). The location of the thimerosal Hg atom near the
Cys408 in the open conformation is shown as a magenta ball. The
side-chains of His233, Arg296, Glu407 and Trp465 are shown
explicitly with the hydrogen bonds marked in broken lines. The
+2 and +1 sugars are also shown.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
337,
367-386)
copyright 2004.
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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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Z.H.Elmabrouk,
F.Vincent,
M.Zhang,
N.L.Smith,
J.P.Turkenburg,
S.J.Charnock,
G.W.Black,
and
E.J.Taylor
(2011).
Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations.
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Proteins,
79,
965-974.
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PDB codes:
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M.L.Garron,
and
M.Cygler
(2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
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Glycobiology,
20,
1547-1573.
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T.V.Vuong,
and
D.B.Wilson
(2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
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Biotechnol Bioeng,
107,
195-205.
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A.Ochiai,
T.Itoh,
B.Mikami,
W.Hashimoto,
and
K.Murata
(2009).
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases.
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J Biol Chem,
284,
10181-10189.
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PDB codes:
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B.Pacheco,
M.Maccarana,
D.R.Goodlett,
A.Malmström,
and
L.Malmström
(2009).
Identification of the Active Site of DS-epimerase 1 and Requirement of N-Glycosylation for Enzyme Function.
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J Biol Chem,
284,
1741-1747.
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V.Prabhakar,
I.Capila,
V.Soundararajan,
R.Raman,
and
R.Sasisekharan
(2009).
Recombinant Expression, Purification, and Biochemical Characterization of Chondroitinase ABC II from Proteus vulgaris.
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J Biol Chem,
284,
974-982.
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G.J.Sathisha,
Y.K.Prakash,
V.B.Chachadi,
N.N.Nagaraja,
S.R.Inamdar,
D.D.Leonidas,
H.S.Savithri,
and
B.M.Swamy
(2008).
X-ray sequence ambiguities of Sclerotium rolfsii lectin resolved by mass spectrometry.
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Amino Acids,
35,
309-320.
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A.Ochiai,
T.Itoh,
Y.Maruyama,
A.Kawamata,
B.Mikami,
W.Hashimoto,
and
K.Murata
(2007).
A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.
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J Biol Chem,
282,
37134-37145.
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PDB codes:
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C.S.Rye,
A.Matte,
M.Cygler,
and
S.G.Withers
(2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.
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Chembiochem,
7,
631-637.
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D.Shaya,
A.Tocilj,
Y.Li,
J.Myette,
G.Venkataraman,
R.Sasisekharan,
and
M.Cygler
(2006).
Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product.
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J Biol Chem,
281,
15525-15535.
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PDB codes:
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T.Itoh,
W.Hashimoto,
B.Mikami,
and
K.Murata
(2006).
Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism.
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J Biol Chem,
281,
29807-29816.
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PDB codes:
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V.L.Yip,
and
S.G.Withers
(2006).
Breakdown of oligosaccharides by the process of elimination.
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Curr Opin Chem Biol,
10,
147-155.
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A.L.Lovering,
S.S.Lee,
Y.W.Kim,
S.G.Withers,
and
N.C.Strynadka
(2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
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J Biol Chem,
280,
2105-2115.
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PDB codes:
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N.L.Smith,
E.J.Taylor,
A.M.Lindsay,
S.J.Charnock,
J.P.Turkenburg,
E.J.Dodson,
G.J.Davies,
and
G.W.Black
(2005).
Structure of a group A streptococcal phage-encoded virulence factor reveals a catalytically active triple-stranded beta-helix.
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Proc Natl Acad Sci U S A,
102,
17652-17657.
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PDB code:
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G.Michel,
K.Pojasek,
Y.Li,
T.Sulea,
R.J.Linhardt,
R.Raman,
V.Prabhakar,
R.Sasisekharan,
and
M.Cygler
(2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
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J Biol Chem,
279,
32882-32896.
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PDB codes:
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S.S.Rajan,
X.Yang,
F.Collart,
V.L.Yip,
S.G.Withers,
A.Varrot,
J.Thompson,
G.J.Davies,
and
W.F.Anderson
(2004).
Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis.
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Structure,
12,
1619-1629.
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PDB code:
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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.
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Links
