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4h2w

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Revision as of 07:56, 3 November 2022

Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and AMP

Structural highlights

4h2w is a 4 chain structure with sequence from Agrobacterium fabrum str. C58 and Bradyrhizobium diazoefficiens USDA 110. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AACL1_BRADU Catalyzes the ATP-dependent activation of L-glycine and its transfer to the phosphopantetheine prosthetic group covalently attached to the vicinal carrier protein bsr0959 of yet unknown function. May participate in nonribosomal peptide synthesis or related processes. L-alanine is a poor substrate whereas L-serine or D-amino acids are not substrates for ATP-dependent activation. Does not display tRNA aminoacylation activity.^[1]

Publication Abstract from PubMed

Amino acid:[carrier protein] ligases (aa:CP ligases) are recently discovered enzymes that are highly similar to class II aminoacyl-tRNA synthetases (aaRSs). However, while aaRSs aminoacylate tRNA and supply building blocks for ribosomal translation, aa:CP ligases transfer activated amino acids to the phosphopantetheine group of small carrier proteins. We have solved the crystal structure of an aa:CP ligase complexed with the carrier protein (CP). The CP prosthetic group enters the active site from a different direction than tRNA in class II aaRS complexes through an idiosyncratic tunnel. CP binds to aa:CP ligase in a fundamentally different manner compared to tRNA binding by structurally closely related aaRSs. Based on crystallographic analysis, an enzyme of altered CP specificity was designed, and the mechanism of amino acid transfer to the prosthetic group was proposed. The presented study reveals how a conserved class II aaRS catalytic core can adapt to another function through minor structural alterations.

Adaptation of Aminoacyl-tRNA Synthetase Catalytic Core to Carrier Protein Aminoacylation.,Mocibob M, Ivic N, Luic M, Weygand-Durasevic I Structure. 2013 Mar 26. pii: S0969-2126(13)00058-0. doi:, 10.1016/j.str.2013.02.017. PMID:23541895^[2]

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

References

↑ Mocibob M, Ivic N, Bilokapic S, Maier T, Luic M, Ban N, Weygand-Durasevic I. Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14585-90. Epub 2010 Jul 27. PMID:20663952 doi:10.1073/pnas.1007470107
↑ Mocibob M, Ivic N, Luic M, Weygand-Durasevic I. Adaptation of Aminoacyl-tRNA Synthetase Catalytic Core to Carrier Protein Aminoacylation. Structure. 2013 Mar 26. pii: S0969-2126(13)00058-0. doi:, 10.1016/j.str.2013.02.017. PMID:23541895 doi:10.1016/j.str.2013.02.017

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4h2w"

@@ Line 1: / Line 1: @@
 ==Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and AMP==
-<StructureSection load='4h2w' size='340' side='right' caption='[[4h2w]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='4h2w' size='340' side='right'caption='[[4h2w]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4h2w]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrfc Agrfc] and [http://en.wikipedia.org/wiki/Bradu Bradu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H2W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4h2w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58] and [https://en.wikipedia.org/wiki/Bradyrhizobium_diazoefficiens_USDA_110 Bradyrhizobium diazoefficiens USDA 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H2W FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PNS:4-PHOSPHOPANTETHEINE'>PNS</scene>, <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=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PNS:4-PHOSPHOPANTETHEINE'>PNS</scene>, <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">[[3mf2|3mf2]], [[4h2s|4h2s]], [[4h2t|4h2t]], [[4h2u|4h2u]], [[4h2v|4h2v]], [[4h2x|4h2x]], [[4h2y|4h2y]]</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=4h2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h2w OCA], [https://pdbe.org/4h2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h2w RCSB], [https://www.ebi.ac.uk/pdbsum/4h2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h2w ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Atu2573,AGR_C_4663 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224911 BRADU]), AGR_C_4658, Atu2571 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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=4h2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h2w OCA], [http://pdbe.org/4h2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h2w RCSB], [http://www.ebi.ac.uk/pdbsum/4h2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h2w ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AACL1_BRAJA AACL1_BRAJA]] Catalyzes the ATP-dependent activation of L-glycine and its transfer to the phosphopantetheine prosthetic group covalently attached to the vicinal carrier protein bsr0959 of yet unknown function. May participate in nonribosomal peptide synthesis or related processes. L-alanine is a poor substrate whereas L-serine or D-amino acids are not substrates for ATP-dependent activation. Does not display tRNA aminoacylation activity. [[http://www.uniprot.org/uniprot/AACP_AGRT5 AACP_AGRT5]] Aminoacyl carrier protein. Can be charged with L-alanine, L-glycine or L-serine, via the formation of a thioester bond between the amino acid and the 4'-phosphopantetheinyl prosthetic group, catalyzed by the Atu2573 ligase.
+[https://www.uniprot.org/uniprot/AACL1_BRADU AACL1_BRADU] Catalyzes the ATP-dependent activation of L-glycine and its transfer to the phosphopantetheine prosthetic group covalently attached to the vicinal carrier protein bsr0959 of yet unknown function. May participate in nonribosomal peptide synthesis or related processes. L-alanine is a poor substrate whereas L-serine or D-amino acids are not substrates for ATP-dependent activation. Does not display tRNA aminoacylation activity.<ref>PMID:20663952</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Agrfc]]
+[[Category: Agrobacterium fabrum str. C58]]
-[[Category: Bradu]]
+[[Category: Bradyrhizobium diazoefficiens USDA 110]]
-[[Category: Ivic, N]]
+[[Category: Large Structures]]
-[[Category: Luic, M]]
+[[Category: Ivic N]]
-[[Category: Mocibob, M]]
+[[Category: Luic M]]
-[[Category: Weygand-Durasevic, I]]
+[[Category: Mocibob M]]
-[[Category: Aminoacyl-trna synthetase]]
+[[Category: Weygand-Durasevic I]]
-[[Category: Atp binding]]
-[[Category: Carrier protein]]
-[[Category: Glycine binding]]
-[[Category: Ligase]]
-[[Category: Seryl-trna synthetase]]

4h2w

From Proteopedia

Revision as of 07:56, 3 November 2022

Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and AMP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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