|
|
Line 3: |
Line 3: |
| <StructureSection load='1xp4' size='340' side='right'caption='[[1xp4]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='1xp4' size='340' side='right'caption='[[1xp4]], [[Resolution|resolution]] 2.80Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XP4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1xp4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_R6 Streptococcus pneumoniae R6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XP4 FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
- | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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">dacA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=171101 STRR6])</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=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [https://pdbe.org/1xp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [https://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 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/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>
| + | |
- | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xp4 OCA], [http://pdbe.org/1xp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xp4 RCSB], [http://www.ebi.ac.uk/pdbsum/1xp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xp4 ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| + | == Function == |
| + | [https://www.uniprot.org/uniprot/Q8DQ99_STRR6 Q8DQ99_STRR6] |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
Line 34: |
Line 34: |
| </StructureSection> | | </StructureSection> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]] | + | [[Category: Streptococcus pneumoniae R6]] |
- | [[Category: Strr6]] | + | [[Category: Dessen A]] |
- | [[Category: Dessen, A]] | + | [[Category: Di Guilmi AM]] |
- | [[Category: Dideberg, O]] | + | [[Category: Dideberg O]] |
- | [[Category: Gouellec, A Le]] | + | [[Category: Le Gouellec A]] |
- | [[Category: Guilmi, A M.Di]]
| + | [[Category: Morlot C]] |
- | [[Category: Morlot, C]] | + | [[Category: Pernot L]] |
- | [[Category: Pernot, L]] | + | [[Category: Vernet T]] |
- | [[Category: Vernet, T]] | + | |
- | [[Category: Five-stranded antiparallel beta-sheet]]
| + | |
- | [[Category: Hydrolase]]
| + | |
- | [[Category: Omega-like loop]]
| + | |
| Structural highlights
Function
Q8DQ99_STRR6
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
Penicillin-binding proteins (PBPs) are membrane-associated enzymes which perform critical functions in the bacterial cell division process. The single d-Ala,d-Ala (d,d)-carboxypeptidase in Streptococcus pneumoniae, PBP3, has been shown to play a key role in control of availability of the peptidoglycal substrate during cell growth. Here, we have biochemically characterized and solved the crystal structure of a soluble form of PBP3 to 2.8 A resolution. PBP3 folds into an NH(2)-terminal, d,d-carboxypeptidase-like domain, and a COOH-terminal, elongated beta-rich region. The carboxypeptidase domain harbors the classic signature of the penicilloyl serine transferase superfamily, in that it contains a central, five-stranded antiparallel beta-sheet surrounded by alpha-helices. As in other carboxypeptidases, which are present in species whose peptidoglycan stem peptide has a lysine residue at the third position, PBP3 has a 14-residue insertion at the level of its omega loop, a feature that distinguishes it from carboxypeptidases from bacteria whose peptidoglycan harbors a diaminopimelate moiety at this position. PBP3 performs substrate acylation in a highly efficient manner (k(cat)/K(m) = 50,500 M(-1) x s(-1)), an event that may be linked to role in control of pneumococcal peptidoglycan reticulation. A model that places PBP3 poised vertically on the bacterial membrane suggests that its COOH-terminal region could act as a pedestal, placing the active site in proximity to the peptidoglycan and allowing the protein to "skid" on the surface of the membrane, trimming pentapeptides during the cell growth and division processes.
Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae.,Morlot C, Pernot L, Le Gouellec A, Di Guilmi AM, Vernet T, Dideberg O, Dessen A J Biol Chem. 2005 Apr 22;280(16):15984-91. Epub 2004 Dec 13. PMID:15596446[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Morlot C, Pernot L, Le Gouellec A, Di Guilmi AM, Vernet T, Dideberg O, Dessen A. Crystal structure of a peptidoglycan synthesis regulatory factor (PBP3) from Streptococcus pneumoniae. J Biol Chem. 2005 Apr 22;280(16):15984-91. Epub 2004 Dec 13. PMID:15596446 doi:10.1074/jbc.M408446200
|