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| | ==1.9 angstrom crystal structure of the active form of the C5a peptidase from Streptococcus pyogenes (ScpA)== | | ==1.9 angstrom crystal structure of the active form of the C5a peptidase from Streptococcus pyogenes (ScpA)== |
| - | <StructureSection load='3eif' size='340' side='right' caption='[[3eif]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='3eif' size='340' side='right'caption='[[3eif]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3eif]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_scarlatinae"_klein_1884 "micrococcus scarlatinae" klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EIF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EIF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3eif]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_scarlatinae"_klein_1884 "micrococcus scarlatinae" klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EIF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">scpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1314 "Micrococcus scarlatinae" Klein 1884])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">scpA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1314 "Micrococcus scarlatinae" Klein 1884])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/C5a_peptidase C5a peptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.110 3.4.21.110] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/C5a_peptidase C5a peptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.110 3.4.21.110] </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=3eif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eif OCA], [http://pdbe.org/3eif PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eif RCSB], [http://www.ebi.ac.uk/pdbsum/3eif PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eif ProSAT]</span></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=3eif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eif OCA], [https://pdbe.org/3eif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eif RCSB], [https://www.ebi.ac.uk/pdbsum/3eif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eif ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | [[Category: Micrococcus scarlatinae klein 1884]] | | [[Category: Micrococcus scarlatinae klein 1884]] |
| | [[Category: C5a peptidase]] | | [[Category: C5a peptidase]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Connell, M R.O]] | | [[Category: Connell, M R.O]] |
| | [[Category: Cooney, J C]] | | [[Category: Cooney, J C]] |
| Structural highlights
3eif is a 1 chain structure with sequence from "micrococcus_scarlatinae"_klein_1884 "micrococcus scarlatinae" klein 1884. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , |
| Gene: | scpA ("Micrococcus scarlatinae" Klein 1884) |
| Activity: | C5a peptidase, with EC number 3.4.21.110 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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
The crystal structure of an active form of ScpA has been solved to 1.9 A resolution. ScpA is a multidomain cell-envelope subtilase from Streptococcus pyogenes that cleaves complement component C5a. The catalytic triad of ScpA is geometrically consistent with other subtilases, clearly demonstrating that the additional activation mechanism proposed for the Streptococcus agalactiae homologue (ScpB) is not required for ScpA. The ScpA structure revealed that access to the catalytic site is restricted by variable regions in the catalytic domain (vr7, vr9, and vr11) and by the presence of the inserted protease-associated (PA) domain and the second fibronectin type III domains (Fn2). Modeling of the ScpA-C5a complex indicates that the substrate binds with carboxyl-terminal residues (65-74) extended through the active site and core residues (1-64) forming exosite-type interactions with the Fn2 domain. This is reminiscent of the two-site mechanism proposed for C5a binding to its receptor. In the nonprime region of the active site, interactions with the substrate backbone are predicted to be more similar to those observed in kexins, involving a single beta-strand in the peptidase. However, in contrast to kexins, there would be diminished emphasis on side-chain interactions, with little charged character in the S3-S1 and S6-S4 subsites occupied by the side chains of residues in vr7 and vr9. Substrate binding is anticipated to be dominated by ionic interactions in two distinct regions of ScpA. On the prime side of the active site, salt bridges are predicted between P1', P2', and P7' residues, and residues in the catalytic and PA domains. Remote to the active site, a larger number of ionic interactions between residues in the C5a core and the Fn2 domain are observed in the model. Thus, both PA and Fn2 domains are expected to play significant roles in substrate recognition.
Model for substrate interactions in C5a peptidase from Streptococcus pyogenes: A 1.9 A crystal structure of the active form of ScpA.,Kagawa TF, O'Connell MR, Mouat P, Paoli M, O'Toole PW, Cooney JC J Mol Biol. 2009 Feb 27;386(3):754-72. Epub 2009 Jan 6. PMID:19152799[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kagawa TF, O'Connell MR, Mouat P, Paoli M, O'Toole PW, Cooney JC. Model for substrate interactions in C5a peptidase from Streptococcus pyogenes: A 1.9 A crystal structure of the active form of ScpA. J Mol Biol. 2009 Feb 27;386(3):754-72. Epub 2009 Jan 6. PMID:19152799 doi:10.1016/j.jmb.2008.12.074
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