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6ez3

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Structure of CDPS from Staphylococcus haemolyticus

Structural highlights

6ez3 is a 6 chain structure with sequence from Staphylococcus haemolyticus JCSC1435. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDLS_STAHJ It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and L-methionine, into cyclodipeptides.^[1]

Publication Abstract from PubMed

Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines. It was shown that CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. However, current understanding of CDPSs only comes from studies of enzymes from the NYH subfamily. The present study reveals the crystal structures of three CDPSs from the XYP subfamily. Comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold. This gives a structural basis for the partition of CDPSs into two subfamilies. Despite these differences, the catalytic residues adopt similar positioning regardless of the subfamily suggesting that the XYP and NYH motifs correspond to two structural solutions to facilitate the reactivity of the catalytic serine residue.

Structural basis for partition of the cyclodipeptide synthases into two subfamilies.,Bourgeois G, Seguin J, Babin M, Belin P, Moutiez M, Mechulam Y, Gondry M, Schmitt E J Struct Biol. 2018 Jul;203(1):17-26. doi: 10.1016/j.jsb.2018.03.001. Epub 2018, Mar 2. PMID:29505829^[2]

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

References

↑ Gondry M, Sauguet L, Belin P, Thai R, Amouroux R, Tellier C, Tuphile K, Jacquet M, Braud S, Courcon M, Masson C, Dubois S, Lautru S, Lecoq A, Hashimoto S, Genet R, Pernodet JL. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat Chem Biol. 2009 Jun;5(6):414-20. doi: 10.1038/nchembio.175. PMID:19430487 doi:http://dx.doi.org/10.1038/nchembio.175
↑ Bourgeois G, Seguin J, Babin M, Belin P, Moutiez M, Mechulam Y, Gondry M, Schmitt E. Structural basis for partition of the cyclodipeptide synthases into two subfamilies. J Struct Biol. 2018 Jul;203(1):17-26. doi: 10.1016/j.jsb.2018.03.001. Epub 2018, Mar 2. PMID:29505829 doi:http://dx.doi.org/10.1016/j.jsb.2018.03.001

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/6ez3"

Categories: Large Structures | Staphylococcus haemolyticus JCSC1435 | Bourgeois G | Mechulam Y | Schmitt E

@@ Line 1: / Line 1: @@
 ==Structure of CDPS from Staphylococcus haemolyticus==
-<StructureSection load='6ez3' size='340' side='right' caption='[[6ez3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='6ez3' size='340' side='right'caption='[[6ez3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ez3]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ez3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_haemolyticus_JCSC1435 Staphylococcus haemolyticus JCSC1435]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EZ3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q24|4q24]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyclo(L-leucyl-L-leucyl)_synthase Cyclo(L-leucyl-L-leucyl) synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.22 2.3.2.22] </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=6ez3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez3 OCA], [https://pdbe.org/6ez3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ez3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ez3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez3 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=6ez3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez3 OCA], [http://pdbe.org/6ez3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ez3 RCSB], [http://www.ebi.ac.uk/pdbsum/6ez3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CDLS_STAHJ CDLS_STAHJ]] It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and L-methionine, into cyclodipeptides.<ref>PMID:19430487</ref>
+[https://www.uniprot.org/uniprot/CDLS_STAHJ CDLS_STAHJ] It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and L-methionine, into cyclodipeptides.<ref>PMID:19430487</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bourgeois, G]]
+[[Category: Large Structures]]
-[[Category: Mechulam, Y]]
+[[Category: Staphylococcus haemolyticus JCSC1435]]
-[[Category: Schmitt, E]]
+[[Category: Bourgeois G]]
-[[Category: Cyclodipeptide]]
+[[Category: Mechulam Y]]
-[[Category: Rna binding protein]]
+[[Category: Schmitt E]]
-[[Category: Trna]]

6ez3

From Proteopedia

Current revision

Structure of CDPS from Staphylococcus haemolyticus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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