4j4m: Difference between revisions

Revision as of 21:32, 16 November 2022

Crystal structure of TM-1, a Trimeresurus mucrosquamatus venom metalloproteinase

Structural highlights

4j4m is a 2 chain structure with sequence from Protobothrops mucrosquamatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VM1T1_PROMU Potent fibrinogenolytic protease which cleaves mainly the Aalpha (FGA) and Bbeta (FGB) chains of fibrinogen and slightly the gamma chain (FGG) (PubMed:8193588, PubMed:7488093). Shows preference for substrates having a moderate-size and hydrophobic residue at the P1' position. Preferentially cleaves Ala-|-Leu and Tyr-|-Leu bonds (PubMed:23732127). Is more susceptible to tripeptide inhibitors than TM-3 (AC O57413) (PubMed:9703966).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The crystal structure of TM-1, a P-I class snake-venom metalloproteinase (SVMP) from the Trimeresurus mucrosquamatus venom, was determined at 1.8-A resolution. The structure exhibits the typical feature of SVMPs and is stabilized by three disulfide linkages. The active site shows a deep S1' substrate-binding pocket limited by the non-conserved Pro174 at the bottom. Further comparisons with other SVMPs suggest that the deep S1' site of TM-1 correlates with its high inhibition sensitivity to the endogenous tripeptide inhibitors. Proteolytic specificity analysis revealed that TM-1 prefers substrates having a moderate-size and hydrophobic residue at the P1' position, consistent with our structural observation.

Crystal structure of a Trimeresurus mucrosquamatus venom metalloproteinase providing new insights into the inhibition by endogenous tripeptide inhibitors.,Chou TL, Wu CH, Huang KF, Wang AH Toxicon. 2013 Sep;71:140-6. doi: 10.1016/j.toxicon.2013.05.009. Epub 2013 May 31. PMID:23732127^[5]

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

References

↑ Chou TL, Wu CH, Huang KF, Wang AH. Crystal structure of a Trimeresurus mucrosquamatus venom metalloproteinase providing new insights into the inhibition by endogenous tripeptide inhibitors. Toxicon. 2013 Sep;71:140-6. doi: 10.1016/j.toxicon.2013.05.009. Epub 2013 May 31. PMID:23732127 doi:10.1016/j.toxicon.2013.05.009
↑ Huang KF, Hung CC, Pan FM, Chow LP, Tsugita A, Chiou SH. Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus): protein microsequencing coupled with cDNA sequence analysis. Biochem Biophys Res Commun. 1995 Nov 2;216(1):223-33. doi:, 10.1006/bbrc.1995.2614. PMID:7488093 doi:https://dx.doi.org/10.1006/bbrc.1995.2614
↑ Huang KF, Hung CC, Chiou SH. Characterization of three fibrinogenolytic proteases isolated from the venom of Taiwan habu (Trimeresurus mucrosquamatus). Biochem Mol Biol Int. 1993 Dec;31(6):1041-50. PMID:8193588
↑ Huang KF, Hung CC, Wu SH, Chiou SH. Characterization of three endogenous peptide inhibitors for multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus). Biochem Biophys Res Commun. 1998 Jul 30;248(3):562-8. doi:, 10.1006/bbrc.1998.9017. PMID:9703966 doi:https://dx.doi.org/10.1006/bbrc.1998.9017
↑ Chou TL, Wu CH, Huang KF, Wang AH. Crystal structure of a Trimeresurus mucrosquamatus venom metalloproteinase providing new insights into the inhibition by endogenous tripeptide inhibitors. Toxicon. 2013 Sep;71:140-6. doi: 10.1016/j.toxicon.2013.05.009. Epub 2013 May 31. PMID:23732127 doi:10.1016/j.toxicon.2013.05.009

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Chou TL, Wu CH, Huang KF, Wang AH. Crystal structure of a Trimeresurus mucrosquamatus venom metalloproteinase providing new insights into the inhibition by endogenous tripeptide inhibitors. Toxicon. 2013 Sep;71:140-6. doi: 10.1016/j.toxicon.2013.05.009. Epub 2013 May 31. PMID:23732127 doi:10.1016/j.toxicon.2013.05.009

[2] Huang KF, Hung CC, Pan FM, Chow LP, Tsugita A, Chiou SH. Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus): protein microsequencing coupled with cDNA sequence analysis. Biochem Biophys Res Commun. 1995 Nov 2;216(1):223-33. doi:, 10.1006/bbrc.1995.2614. PMID:7488093 doi:https://dx.doi.org/10.1006/bbrc.1995.2614

[3] Huang KF, Hung CC, Chiou SH. Characterization of three fibrinogenolytic proteases isolated from the venom of Taiwan habu (Trimeresurus mucrosquamatus). Biochem Mol Biol Int. 1993 Dec;31(6):1041-50. PMID:8193588

[4] Huang KF, Hung CC, Wu SH, Chiou SH. Characterization of three endogenous peptide inhibitors for multiple metalloproteinases with fibrinogenolytic activity from the venom of Taiwan habu (Trimeresurus mucrosquamatus). Biochem Biophys Res Commun. 1998 Jul 30;248(3):562-8. doi:, 10.1006/bbrc.1998.9017. PMID:9703966 doi:https://dx.doi.org/10.1006/bbrc.1998.9017

[5] Chou TL, Wu CH, Huang KF, Wang AH. Crystal structure of a Trimeresurus mucrosquamatus venom metalloproteinase providing new insights into the inhibition by endogenous tripeptide inhibitors. Toxicon. 2013 Sep;71:140-6. doi: 10.1016/j.toxicon.2013.05.009. Epub 2013 May 31. PMID:23732127 doi:10.1016/j.toxicon.2013.05.009

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[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='4j4m' size='340' side='right'caption='[[4j4m]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4j4m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J4M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J4M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4j4m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Protobothrops_mucrosquamatus Protobothrops mucrosquamatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J4M FirstGlance]. <br>
-</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>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kuf|1kuf]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4j4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j4m OCA], [https://pdbe.org/4j4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j4m RCSB], [https://www.ebi.ac.uk/pdbsum/4j4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j4m ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trimerelysin_II Trimerelysin II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.53 3.4.24.53] </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=4j4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j4m OCA], [http://pdbe.org/4j4m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j4m RCSB], [http://www.ebi.ac.uk/pdbsum/4j4m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j4m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/VM1T1_PROMU VM1T1_PROMU] Potent fibrinogenolytic protease which cleaves mainly the Aalpha (FGA) and Bbeta (FGB) chains of fibrinogen and slightly the gamma chain (FGG) (PubMed:8193588, PubMed:7488093). Shows preference for substrates having a moderate-size and hydrophobic residue at the P1' position. Preferentially cleaves Ala-|-Leu and Tyr-|-Leu bonds (PubMed:23732127). Is more susceptible to tripeptide inhibitors than TM-3 (AC O57413) (PubMed:9703966).<ref>PMID:23732127</ref> <ref>PMID:7488093</ref> <ref>PMID:8193588</ref> <ref>PMID:9703966</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 [[Category: Large Structures]]
 [[Category: Protobothrops mucrosquamatus]]
-[[Category: Trimerelysin II]]
+[[Category: Chou TL]]
-[[Category: Chou, T L]]
+[[Category: Huang KF]]
-[[Category: Huang, K F]]
+[[Category: Wang AH]]
-[[Category: Wang, A H]]
+[[Category: Wu CH]]
-[[Category: Wu, C H]]
-[[Category: Alpha/beta-mixed fold]]
-[[Category: Endopeptidase]]
-[[Category: Hydrolase]]

4j4m: Difference between revisions

Revision as of 21:32, 16 November 2022

Crystal structure of TM-1, a Trimeresurus mucrosquamatus venom metalloproteinase

Structural highlights

Function

Publication Abstract from PubMed

References

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