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{{STRUCTURE_4h2x|  PDB=4h2x  |  SCENE=  }}
===Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylate===
{{ABSTRACT_PUBMED_23541895}}


==Function==
==Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylate==
[[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.  
<StructureSection load='4h2x' size='340' side='right'caption='[[4h2x]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4h2x]] 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=4H2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H2X FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=G5A:5-O-(GLYCYLSULFAMOYL)ADENOSINE'>G5A</scene>, <scene name='pdbligand=PNS:4-PHOSPHOPANTETHEINE'>PNS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4h2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h2x OCA], [https://pdbe.org/4h2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h2x RCSB], [https://www.ebi.ac.uk/pdbsum/4h2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h2x ProSAT]</span></td></tr>
</table>
== Function ==
[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 ==
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.


==About this Structure==
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<ref>PMID:23541895</ref>
[[4h2x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._c58 Agrobacterium fabrum str. c58] and [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum_usda_110 Bradyrhizobium japonicum usda 110]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H2X OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<ref group="xtra">PMID:020663952</ref><references group="xtra"/><references/>
</div>
[[Category: Agrobacterium fabrum str. c58]]
<div class="pdbe-citations 4h2x" style="background-color:#fffaf0;"></div>
[[Category: Bradyrhizobium japonicum usda 110]]
== References ==
[[Category: Ivic, N.]]
<references/>
[[Category: Luic, M.]]
__TOC__
[[Category: Mocibob, M.]]
</StructureSection>
[[Category: Weygand-Durasevic, I.]]
[[Category: Agrobacterium fabrum str. C58]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Bradyrhizobium diazoefficiens USDA 110]]
[[Category: Atp binding]]
[[Category: Large Structures]]
[[Category: Carrier protein]]
[[Category: Ivic N]]
[[Category: Glycine binding]]
[[Category: Luic M]]
[[Category: Ligase]]
[[Category: Mocibob M]]
[[Category: Seryl-trna synthetase]]
[[Category: Weygand-Durasevic I]]

Latest revision as of 10:56, 3 November 2022

Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylateCrystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylate

Structural highlights

4h2x 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

  1. ↑ 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
  2. ↑ 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

4h2x, resolution 2.15Å

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