1nd1

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Revision as of 10:18, 25 October 2017

Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.

Structural highlights

1nd1 is a 1 chain structure with sequence from Bothrops asper. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[VM1B1_BOTAS] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

BaP1 is a 22.7-kD P-I-type zinc-dependent metalloproteinase isolated from the venom of the snake Bothrops asper, a medically relevant species in Central America. This enzyme exerts multiple tissue-damaging activities, including hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. BaP1 is a single chain of 202 amino acids that shows highest sequence identity with metalloproteinases isolated from the venoms of snakes of the subfamily Crotalinae. It has six Cys residues involved in three disulfide bridges (Cys 117-Cys 197, Cys 159-Cys 181, Cys 157-Cys 164). It has the consensus sequence H(142)E(143)XXH(146)XXGXXH(152), as well as the sequence C(164)I(165)M(166), which characterize the "metzincin" superfamily of metalloproteinases. The active-site cleft separates a major subdomain (residues 1-152), comprising four alpha-helices and a five-stranded beta-sheet, from the minor subdomain, which is formed by a single alpha-helix and several loops. The catalytic zinc ion is coordinated by the N(epsilon 2) nitrogen atoms of His 142, His 146, and His 152, in addition to a solvent water molecule, which in turn is bound to Glu 143. Several conserved residues contribute to the formation of the hydrophobic pocket, and Met 166 serves as a hydrophobic base for the active-site groups. Sequence and structural comparisons of hemorrhagic and nonhemorrhagic P-I metalloproteinases from snake venoms revealed differences in several regions. In particular, the loop comprising residues 153 to 176 has marked structural differences between metalloproteinases with very different hemorrhagic activities. Because this region lies in close proximity to the active-site microenvironment, it may influence the interaction of these enzymes with physiologically relevant substrates in the extracellular matrix.

Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.,Watanabe L, Shannon JD, Valente RH, Rucavado A, Alape-Giron A, Kamiguti AS, Theakston RD, Fox JW, Gutierrez JM, Arni RK Protein Sci. 2003 Oct;12(10):2273-81. PMID:14500885^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Farsky SH, Goncalves LR, Gutierrez JM, Correa AP, Rucavado A, Gasque P, Tambourgi DV. Bothrops asper snake venom and its metalloproteinase BaP-1 activate the complement system. Role in leucocyte recruitment. Mediators Inflamm. 2000;9(5):213-21. PMID:11200361 doi:http://dx.doi.org/10.1080/09629350020025728
↑ Patino AC, Pereanez JA, Nunez V, Benjumea DM, Fernandez M, Rucavado A, Sanz L, Calvete JJ. Isolation and biological characterization of Batx-I, a weak hemorrhagic and fibrinogenolytic PI metalloproteinase from Colombian Bothrops atrox venom. Toxicon. 2010 Nov;56(6):936-43. doi: 10.1016/j.toxicon.2010.06.016. Epub 2010 Jun, 30. PMID:20600221 doi:http://dx.doi.org/10.1016/j.toxicon.2010.06.016
↑ Bernardes CP, Menaldo DL, Camacho E, Rosa JC, Escalante T, Rucavado A, Lomonte B, Gutierrez JM, Sampaio SV. Proteomic analysis of Bothrops pirajai snake venom and characterization of BpirMP, a new P-I metalloproteinase. J Proteomics. 2013 Mar 27;80:250-67. doi: 10.1016/j.jprot.2013.01.021. Epub 2013 , Feb 4. PMID:23385358 doi:http://dx.doi.org/10.1016/j.jprot.2013.01.021
↑ Gutierrez JM, Romero M, Diaz C, Borkow G, Ovadia M. Isolation and characterization of a metalloproteinase with weak hemorrhagic activity from the venom of the snake Bothrops asper (terciopelo). Toxicon. 1995 Jan;33(1):19-29. PMID:7778126
↑ Watanabe L, Shannon JD, Valente RH, Rucavado A, Alape-Giron A, Kamiguti AS, Theakston RD, Fox JW, Gutierrez JM, Arni RK. Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities. Protein Sci. 2003 Oct;12(10):2273-81. PMID:14500885

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nd1"

@@ Line 1: / Line 1: @@
 ==Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.==
 <StructureSection load='1nd1' size='340' side='right' caption='[[1nd1]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd1 OCA], [http://pdbe.org/1nd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nd1 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd1 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd1 OCA], [http://pdbe.org/1nd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nd1 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd1 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nd1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

1nd1

From Proteopedia

Revision as of 10:18, 25 October 2017

Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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