3ckm: Difference between revisions
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< | ==LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A== | ||
<StructureSection load='3ckm' size='340' side='right'caption='[[3ckm]], [[Resolution|resolution]] 1.35Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ckm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haein Haein]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2h4a 2h4a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CKM FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5kcn|5kcn]], [[5vat|5vat]], [[5vbg|5vbg]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YraM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=3ckm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ckm OCA], [https://pdbe.org/3ckm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ckm RCSB], [https://www.ebi.ac.uk/pdbsum/3ckm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ckm ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/LPOA_HAEIN LPOA_HAEIN]] Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a). | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ck/3ckm_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<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/main_output.php?pdb_ID=3ckm ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nontypeable Haemophilus influenzae is an obligate human parasite that often causes middle ear infections in children and exacerbates chronic obstructive pulmonary disorder, the fourth leading cause of death in the United States. There are no effective vaccines available for this strain. The lipoprotein YraM (gene HI1655) was identified as essential for the growth and viability of H. influenzae but its function is unknown. Sequence comparisons showed that YraM is a fusion of two protein modules. We grew crystals of the carboxyl-terminal module of YraM comprising residues 257-573 (YraM-C), phased the diffraction data by the multiwavelength anomalous diffraction technique, and refined the model to a crystallographic R-factor of 0.16 (R(free) = 0.19) with data to 1.35 A resolution. The two-domain structure of YraM-C adopts a fold similar to that observed for the open, unliganded forms of several periplasmic binding proteins (PBPs) involved in bacterial active transport. Sequence alignments of YraM homologues from other Gram-negative species showed that the most conserved residues of YraM-C cluster between the two domains in the location where other PBPs bind their cognate ligand. Modeling of YraM-C into a closed conformation similar to the leucine-bound form of the Leu/Ile/Val-binding protein (LIVBP) shows a putative binding pocket larger than the leucine-binding site in LIVBP. The pocket has both polar and nonpolar surfaces, with the latter located in the same area where a leucine side chain binds to LIVBP. We discuss possible biological functions of YraM considering its predicted location in the outer membrane, a novel place for such a binding protein. Proteins 2008. (c) 2008 Wiley-Liss, Inc. | |||
Structure of YraM, a protein essential for growth of Haemophilus influenzae.,Vijayalakshmi J, Akerley BJ, Saper MA Proteins. 2008 Apr 15;. PMID:18412262<ref>PMID:18412262</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ckm" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Haein]] | ||
[[Category: Large Structures]] | |||
[[Category: Saper, M A]] | |||
== | [[Category: Vijayalakshmi, J]] | ||
< | [[Category: Biosynthetic protein]] | ||
[[Category: | |||
[[Category: Saper, M A | |||
[[Category: Vijayalakshmi, J | |||
[[Category: Lipoprotein]] | [[Category: Lipoprotein]] | ||
[[Category: Pbp1a]] | |||
[[Category: Peptidoglycan]] | |||
[[Category: Periplasmic-binding protein]] | [[Category: Periplasmic-binding protein]] | ||
[[Category: | [[Category: Transpeptidase]] | ||
[[Category: Unliganded]] | [[Category: Unliganded]] | ||
[[Category: Yram]] | [[Category: Yram]] | ||
Latest revision as of 10:59, 27 January 2022
LpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1ALpoA (YraM) C-domain from Haemophilus influenzae, a regulator of PBP1A
Structural highlights
Function[LPOA_HAEIN] Regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1A (PBP1a). 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 PubMedNontypeable Haemophilus influenzae is an obligate human parasite that often causes middle ear infections in children and exacerbates chronic obstructive pulmonary disorder, the fourth leading cause of death in the United States. There are no effective vaccines available for this strain. The lipoprotein YraM (gene HI1655) was identified as essential for the growth and viability of H. influenzae but its function is unknown. Sequence comparisons showed that YraM is a fusion of two protein modules. We grew crystals of the carboxyl-terminal module of YraM comprising residues 257-573 (YraM-C), phased the diffraction data by the multiwavelength anomalous diffraction technique, and refined the model to a crystallographic R-factor of 0.16 (R(free) = 0.19) with data to 1.35 A resolution. The two-domain structure of YraM-C adopts a fold similar to that observed for the open, unliganded forms of several periplasmic binding proteins (PBPs) involved in bacterial active transport. Sequence alignments of YraM homologues from other Gram-negative species showed that the most conserved residues of YraM-C cluster between the two domains in the location where other PBPs bind their cognate ligand. Modeling of YraM-C into a closed conformation similar to the leucine-bound form of the Leu/Ile/Val-binding protein (LIVBP) shows a putative binding pocket larger than the leucine-binding site in LIVBP. The pocket has both polar and nonpolar surfaces, with the latter located in the same area where a leucine side chain binds to LIVBP. We discuss possible biological functions of YraM considering its predicted location in the outer membrane, a novel place for such a binding protein. Proteins 2008. (c) 2008 Wiley-Liss, Inc. Structure of YraM, a protein essential for growth of Haemophilus influenzae.,Vijayalakshmi J, Akerley BJ, Saper MA Proteins. 2008 Apr 15;. PMID:18412262[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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