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PDBsum entry 1wni
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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of h2-proteinase
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Structure:
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Trimerelysin ii. Chain: a. Synonym: h2-proteinase, h2 metalloproteinase. Ec: 3.4.24.53
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Source:
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Trimeresurus flavoviridis. Organism_taxid: 88087
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Resolution:
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Authors:
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T.Kumasaka,M.Yamamoto,H.Moriyama,N.Tanaka,M.Sato,Y.Katsube, Y.Yamakawa,T.Omori-Satoh,S.Iwanaga,T.Ueki
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Key ref:
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T.Kumasaka
et al.
(1996).
Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.
J Biochem (tokyo),
119,
49-57.
PubMed id:
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Date:
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04-Aug-04
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Release date:
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17-Aug-04
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PROCHECK
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Headers
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References
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P20165
(VM1T2_PROFL) -
Snake venom metalloproteinase trimerelysin-2 from Protobothrops flavoviridis
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Seq:
Struc:
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201 a.a.
198 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.3.4.24.53
- trimerelysin Ii.
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Reaction:
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Cleavage of 3-Asn-|-Gln-4, 10-His-|-Leu-11 and 14-Ala-|-Leu-15 in the insulin B chain, and the bond Z-Gly-Pro-|-Leu-Gly-Pro in a small molecule substrate of microbial collagenase.
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Cofactor:
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Zn(2+)
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J Biochem (tokyo)
119:49-57
(1996)
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PubMed id:
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Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.
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T.Kumasaka,
M.Yamamoto,
H.Moriyama,
N.Tanaka,
M.Sato,
Y.Katsube,
Y.Yamakawa,
T.Omori-Satoh,
S.Iwanaga,
T.Ueki.
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ABSTRACT
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The crystal structure of the zinc-protease, H2-proteinase, isolated from the
venom of Trimeresurus flavoviridis has been determined. The crystallographic R
factor is 0.176 for 10,635 reflections with Fobs > 2sigma(Fobs) in the 8.0 to
2.2 Angstrom resolution range. The enzyme has two domains with a cleft in which
a catalytic zinc atom is located. The N-terminal domain is composed of four
helices around a central five-stranded beta-sheet. The irregularly folded
C-terminal domain contains one helix and two disulfide bridges. These two
domains are linked by a disulfide bridge. In the zinc environment, the catalytic
zinc atom forms a distorted tetrahedral coordination with three histidines and
one catalytic water molecule, and the methionine-containing turn is structurally
conserved. These are distinctive features of the metzincins, one of the zinc
metalloprotease superfamilies. The entire structure shows good agreement with
that of two Crotalus snake venom proteases, adamalysin II and atrolysin C. The
H2-proteinase, however, contains no structural calcium ions, and differences of
disulfide configurations and the coordination of the catalytic water molecule
exist as compared with the other two proteases.
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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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D.R.Rokyta,
K.P.Wray,
A.R.Lemmon,
E.M.Lemmon,
and
S.B.Caudle
(2011).
A high-throughput venom-gland transcriptome for the Eastern Diamondback Rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes.
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Toxicon,
57,
657-671.
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J.W.Fox,
and
S.M.Serrano
(2008).
Insights into and speculations about snake venom metalloproteinase (SVMP) synthesis, folding and disulfide bond formation and their contribution to venom complexity.
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FEBS J,
275,
3016-3030.
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L.A.Ponce-Soto,
V.L.Bonfim,
J.C.Novello,
R.Navarro Oviedo,
A.Yarlequé Chocas,
and
S.Marangoni
(2007).
Isolation and characterization of a serine protease, Ba III-4, from Peruvian Bothrops atrox venom.
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Protein J,
26,
387-394.
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J.Hou,
M.Li,
J.Chen,
P.Qiu,
X.Liang,
Z.Lou,
Z.Rao,
and
G.Yan
(2005).
Crystallization and preliminary X-ray studies of a non-haemorrhagic fibrin(ogen)olytic metalloproteinase from the venom of Agkistrodon acutus.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
355-358.
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L.Watanabe,
J.D.Shannon,
R.H.Valente,
A.Rucavado,
A.Alape-Girón,
A.S.Kamiguti,
R.D.Theakston,
J.W.Fox,
J.M.Gutiérrez,
and
R.K.Arni
(2003).
Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.
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Protein Sci,
12,
2273-2281.
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PDB code:
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K.F.Huang,
S.H.Chiou,
T.P.Ko,
J.M.Yuann,
and
A.H.Wang
(2002).
The 1.35 A structure of cadmium-substituted TM-3, a snake-venom metalloproteinase from Taiwan habu: elucidation of a TNFalpha-converting enzyme-like active-site structure with a distorted octahedral geometry of cadmium.
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Acta Crystallogr D Biol Crystallogr,
58,
1118-1128.
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PDB code:
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L.Watanabe,
A.Rucavado,
A.Kamiguti,
R.D.Theakston,
J.M.Gutiérrez,
and
R.K.Arni
(2002).
Crystallization and preliminary diffraction data of BaP1, a haemorrhagic metalloproteinase from Bothrops asper snake venom.
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Acta Crystallogr D Biol Crystallogr,
58,
1034-1035.
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M.B.Bolger,
S.Swenson,
and
F.S.Markland
(2001).
Three-dimensional structure of fibrolase, the fibrinolytic enzyme from southern copperhead venom, modeled from the X-ray structure of adamalysin II and atrolysin C.
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AAPS PharmSci,
3,
E16.
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T.Hori,
T.Kumasaka,
M.Yamamoto,
N.Nonaka,
N.Tanaka,
Y.Hashimoto,
U.Ueki,
and
K.Takio
(2001).
Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.
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Acta Crystallogr D Biol Crystallogr,
57,
361-368.
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PDB codes:
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I.H.Tsai,
Y.M.Wang,
T.Y.Chiang,
Y.L.Chen,
and
R.J.Huang
(2000).
Purification, cloning and sequence analyses for pro-metalloprotease-disintegrin variants from Deinagkistrodon acutus venom and subclassification of the small venom metalloproteases.
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Eur J Biochem,
267,
1359-1367.
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J.M.Gutiérrez,
and
A.Rucavado
(2000).
Snake venom metalloproteinases: their role in the pathogenesis of local tissue damage.
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Biochimie,
82,
841-850.
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X.Zhu,
M.Teng,
and
L.Niu
(1999).
Structure of acutolysin-C, a haemorrhagic toxin from the venom of Agkistrodon acutus, providing further evidence for the mechanism of the pH-dependent proteolytic reaction of zinc metalloproteinases.
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Acta Crystallogr D Biol Crystallogr,
55,
1834-1841.
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PDB code:
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K.Maskos,
C.Fernandez-Catalan,
R.Huber,
G.P.Bourenkov,
H.Bartunik,
G.A.Ellestad,
P.Reddy,
M.F.Wolfson,
C.T.Rauch,
B.J.Castner,
R.Davis,
H.R.Clarke,
M.Petersen,
J.N.Fitzner,
D.P.Cerretti,
C.J.March,
R.J.Paxton,
R.A.Black,
and
W.Bode
(1998).
Crystal structure of the catalytic domain of human tumor necrosis factor-alpha-converting enzyme.
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Proc Natl Acad Sci U S A,
95,
3408-3412.
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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
code is
shown on the right.
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Links
