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PDBsum entry 1hm2
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* Residue conservation analysis
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PDB id:
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Lyase
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Title:
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Active site of chondroitinase ac lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis
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Structure:
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Chondroitinase ac. Chain: a. Engineered: yes
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Source:
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Pedobacter heparinus. Organism_taxid: 984. Expressed in: pedobacter heparinus. Expression_system_taxid: 984
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Resolution:
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2.00Å
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R-factor:
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0.233
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R-free:
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0.270
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Authors:
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W.Huang,L.Boju,L.Tkalec,H.Su,H.O.Yang,N.S.Gunay,R.J.Linhardt,Y.S.Kim, A.Matte,M.Cygler
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Key ref:
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W.Huang
et al.
(2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
Biochemistry,
40,
2359-2372.
PubMed id:
DOI:
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Date:
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04-Dec-00
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Release date:
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02-May-01
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PROCHECK
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Headers
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References
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Q59288
(CSLA_PEDHD) -
Chondroitinase-AC from Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3)
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Seq:
Struc:
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700 a.a.
674 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.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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Biochemistry
40:2359-2372
(2001)
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PubMed id:
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Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
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W.Huang,
L.Boju,
L.Tkalec,
H.Su,
H.O.Yang,
N.S.Gunay,
R.J.Linhardt,
Y.S.Kim,
A.Matte,
M.Cygler.
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ABSTRACT
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The crystal structures of Flavobacterium heparinium chondroitin AC lyase
(chondroitinase AC; EC 4.2.2.5) bound to dermatan sulfate hexasaccharide
(DS(hexa)), tetrasaccharide (DS(tetra)), and hyaluronic acid tetrasaccharide
(HA(tetra)) have been refined at 2.0, 2.0, and 2.1 A resolution, respectively.
The structure of the Tyr234Phe mutant of AC lyase bound to a chondroitin sulfate
tetrasaccharide (CS(tetra)) has also been determined to 2.3 A resolution. For
each of these complexes, four (DS(hexa) and CS(tetra)) or two (DS(tetra) and
HA(tetra)) ordered sugars are visible in electron density maps. The lyase AC
DS(hexa) and CS(tetra) complexes reveal binding at four subsites, -2, -1, +1,
and +2, within a narrow and shallow protein channel. We suggest that subsites -2
and -1 together represent the substrate recognition area, +1 is the catalytic
subsite and +1 and +2 together represent the product release area. The putative
catalytic site is located between the substrate recognition area and the product
release area, carrying out catalysis at the +1 subsite. Four residues near the
catalytic site, His225, Tyr234, Arg288, and Glu371 together form a catalytic
tetrad. The mutations His225Ala, Tyr234Phe, Arg288Ala, and Arg292Ala, revealed
residual activity for only the Arg292Ala mutant. Structural data indicate that
Arg292 is primarily involved in recognition of the N-acetyl and sulfate moieties
of galactosamine, but does not participate directly in catalysis. Candidates for
the general base, removing the proton attached to C-5 of the glucuronic acid at
the +1 subsite, are Tyr234, which could be transiently deprotonated during
catalysis, or His225. Tyrosine 234 is a candidate to protonate the leaving
group. Arginine 288 likely contributes to charge neutralization and
stabilization of the enolate anion intermediate during catalysis.
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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.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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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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H.J.Rozeboom,
T.M.Bjerkan,
K.H.Kalk,
H.Ertesvåg,
S.Holtan,
F.L.Aachmann,
S.Valla,
and
B.W.Dijkstra
(2008).
Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.
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J Biol Chem,
283,
23819-23828.
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PDB codes:
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K.Murata,
S.Kawai,
B.Mikami,
and
W.Hashimoto
(2008).
Superchannel of bacteria: biological significance and new horizons.
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Biosci Biotechnol Biochem,
72,
265-277.
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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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R.Sasisekharan,
R.Raman,
and
V.Prabhakar
(2006).
Glycomics approach to structure-function relationships of glycosaminoglycans.
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Annu Rev Biomed Eng,
8,
181-231.
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H.X.Xie,
P.Nie,
M.X.Chang,
Y.Liu,
and
W.J.Yao
(2005).
Gene cloning and functional analysis of glycosaminoglycan-degrading enzyme chondroitin AC lyase from Flavobacterium columnare G4.
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Arch Microbiol,
184,
49-55.
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W.Hashimoto,
K.Momma,
Y.Maruyama,
M.Yamasaki,
B.Mikami,
and
K.Murata
(2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
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Biosci Biotechnol Biochem,
69,
673-692.
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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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O.Miyake,
A.Ochiai,
W.Hashimoto,
and
K.Murata
(2004).
Origin and diversity of alginate lyases of families PL-5 and -7 in Sphingomonas sp. strain A1.
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J Bacteriol,
186,
2891-2896.
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T.Itoh,
S.Akao,
W.Hashimoto,
B.Mikami,
and
K.Murata
(2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
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J Biol Chem,
279,
31804-31812.
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PDB code:
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W.Hashimoto,
M.Yamasaki,
T.Itoh,
K.Momma,
B.Mikami,
and
K.Murata
(2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
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J Biosci Bioeng,
98,
399-413.
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D.J.Rigden,
and
M.J.Jedrzejas
(2003).
Structures of Streptococcus pneumoniae hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides. Insights into specificity and mechanism of action.
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J Biol Chem,
278,
50596-50606.
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PDB codes:
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W.Hashimoto,
H.Nankai,
B.Mikami,
and
K.Murata
(2003).
Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.
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J Biol Chem,
278,
7663-7673.
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PDB codes:
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J.R.Myette,
Z.Shriver,
T.Kiziltepe,
M.W.McLean,
G.Venkataraman,
and
R.Sasisekharan
(2002).
Molecular cloning of the heparin/heparan sulfate delta 4,5 unsaturated glycuronidase from Flavobacterium heparinum, its recombinant expression in Escherichia coli, and biochemical determination of its unique substrate specificity.
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Biochemistry,
41,
7424-7434.
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K.Pojasek,
R.Raman,
P.Kiley,
G.Venkataraman,
and
R.Sasisekharan
(2002).
Biochemical characterization of the chondroitinase B active site.
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J Biol Chem,
277,
31179-31186.
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L.V.Mello,
B.L.De Groot,
S.Li,
and
M.J.Jedrzejas
(2002).
Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan.
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J Biol Chem,
277,
36678-36688.
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PDB code:
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S.J.Charnock,
I.E.Brown,
J.P.Turkenburg,
G.W.Black,
and
G.J.Davies
(2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
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Proc Natl Acad Sci U S A,
99,
12067-12072.
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PDB codes:
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A.J.Day,
and
J.K.Sheehan
(2001).
Hyaluronan: polysaccharide chaos to protein organisation.
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Curr Opin Struct Biol,
11,
617-622.
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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
