6fqb: Difference between revisions

Latest revision as of 09:56, 23 October 2024

MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6

Structural highlights

6fqb is a 8 chain structure with sequence from Streptococcus pneumoniae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	GLN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MURT_STRR6 The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide (PubMed:24044435, PubMed:30093673). The MurT subunit catalyzes the ATP-dependent amidation of D-glutamate residue of lipid II, converting it to an isoglutamine residue (PubMed:30093673).^[1] ^[2]

Publication Abstract from PubMed

The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 A resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.

Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae.,Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Havarstein LS, Zapun A Nat Commun. 2018 Aug 9;9(1):3180. doi: 10.1038/s41467-018-05602-w. PMID:30093673^[3]

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

References

↑ Zapun A, Philippe J, Abrahams KA, Signor L, Roper DI, Breukink E, Vernet T. In vitro reconstitution of peptidoglycan assembly from the Gram-positive pathogen Streptococcus pneumoniae. ACS Chem Biol. 2013 Dec 20;8(12):2688-96. PMID:24044435 doi:10.1021/cb400575t
↑ Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Havarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun. 2018 Aug 9;9(1):3180. doi: 10.1038/s41467-018-05602-w. PMID:30093673 doi:https://dx.doi.org/10.1038/s41467-018-05602-w
↑ Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Havarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun. 2018 Aug 9;9(1):3180. doi: 10.1038/s41467-018-05602-w. PMID:30093673 doi:https://dx.doi.org/10.1038/s41467-018-05602-w

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Zapun A, Philippe J, Abrahams KA, Signor L, Roper DI, Breukink E, Vernet T. In vitro reconstitution of peptidoglycan assembly from the Gram-positive pathogen Streptococcus pneumoniae. ACS Chem Biol. 2013 Dec 20;8(12):2688-96. PMID:24044435 doi:10.1021/cb400575t

[2] Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Havarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun. 2018 Aug 9;9(1):3180. doi: 10.1038/s41467-018-05602-w. PMID:30093673 doi:https://dx.doi.org/10.1038/s41467-018-05602-w

[3] Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Havarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun. 2018 Aug 9;9(1):3180. doi: 10.1038/s41467-018-05602-w. PMID:30093673 doi:https://dx.doi.org/10.1038/s41467-018-05602-w

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6==
-<StructureSection load='6fqb' size='340' side='right' caption='[[6fqb]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='6fqb' size='340' side='right'caption='[[6fqb]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6fqb]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FQB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6fqb]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FQB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLN:GLUTAMINE'>GLN</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]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">A4260_05845, ERS019420_00606, ERS020535_00125, ERS021368_00525, ERS022199_00743, ERS043879_01366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886]), A4260_05840, AWW74_09320, CHL72_09035, CIT24_04835, CS877_04020, CSH34_00860, ERS003549_02292, ERS019166_00428, ERS019416_00232, ERS019420_00605, ERS019499_01955, ERS019595_01427, ERS020136_01107, ERS020137_00292, ERS020140_00887, ERS020142_00808, ERS020143_01959, ERS020147_00746, ERS020148_00821, ERS020178_04008, ERS020408_00223, ERS020474_01302, ERS020521_00204, ERS020522_00778, ERS020523_00656, ERS020524_01042, ERS020526_00540, ERS020526_04035, ERS020527_01973, ERS020528_00148, ERS020541_00600, ERS020692_00332, ERS020827_01405, ERS020831_02169, ERS021300_01369, ERS021447_05442, ERS021629_07046, ERS021762_02260, ERS021858_02776, ERS022045_06260, ERS022071_00358, ERS022199_00742, ERS022232_05365, ERS022363_01901, ERS022390_00924, ERS044004_01668, ERS068943_01580, ERS232497_02277, ERS232498_04930, ERS232508_01880, ERS409064_00176, ERS558328_00424, SAMEA1026345_00620, SAMEA2626854_01213, SAMEA2626872_01126 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylcobyric_acid_synthase_(glutamine-hydrolyzing) Adenosylcobyric acid synthase (glutamine-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.10 6.3.5.10] </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=6fqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fqb OCA], [https://pdbe.org/6fqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fqb RCSB], [https://www.ebi.ac.uk/pdbsum/6fqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fqb ProSAT]</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=6fqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fqb OCA], [http://pdbe.org/6fqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fqb RCSB], [http://www.ebi.ac.uk/pdbsum/6fqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fqb ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MURT_STRR6 MURT_STRR6] The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide (PubMed:24044435, PubMed:30093673). The MurT subunit catalyzes the ATP-dependent amidation of D-glutamate residue of lipid II, converting it to an isoglutamine residue (PubMed:30093673).<ref>PMID:24044435</ref> <ref>PMID:30093673</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 6fqb" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Mur ligase|Mur ligase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Breukink, E]]
+[[Category: Large Structures]]
-[[Category: Contreras-Martel, C]]
+[[Category: Streptococcus pneumoniae]]
-[[Category: Corre, L Le]]
+[[Category: Breukink E]]
-[[Category: Gravier-Pelletier, C]]
+[[Category: Contreras-Martel C]]
-[[Category: Havarstein, L S]]
+[[Category: Gravier-Pelletier C]]
-[[Category: Hegnar, O A]]
+[[Category: Havarstein LS]]
-[[Category: Leisico, F]]
+[[Category: Hegnar OA]]
-[[Category: Morlot, C]]
+[[Category: Le Corre L]]
-[[Category: Peters, K]]
+[[Category: Leisico F]]
-[[Category: Pietrancosta, N]]
+[[Category: Morlot C]]
-[[Category: Simon, N]]
+[[Category: Peters K]]
-[[Category: Straume, D]]
+[[Category: Pietrancosta N]]
-[[Category: Villard, A M]]
+[[Category: Simon N]]
-[[Category: Vollmer, W]]
+[[Category: Straume D]]
-[[Category: Zapun, A]]
+[[Category: Villard AM]]
-[[Category: Amidotransferase]]
+[[Category: Vollmer W]]
-[[Category: Cytosolic]]
+[[Category: Zapun A]]
-[[Category: Ligase]]
-[[Category: Mur family]]

6fqb: Difference between revisions

Latest revision as of 09:56, 23 October 2024

MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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