4q31: Difference between revisions

Latest revision as of 23:05, 26 March 2025

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

Structural highlights

4q31 is a 8 chain structure with sequence from Micromonospora echinospora. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.099Å
Ligands:	CL, FMT, GOL, LLP, MES, MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8KNG3_MICEC

Publication Abstract from PubMed

CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine gamma-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate.,Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN Jr Struct Dyn. 2016 Apr 29;3(3):034702. doi: 10.1063/1.4948539. eCollection 2016, May. PMID:27191010^[1]

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

References

↑ Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN Jr. Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. Struct Dyn. 2016 Apr 29;3(3):034702. doi: 10.1063/1.4948539. eCollection 2016, May. PMID:27191010 doi:https://dx.doi.org/10.1063/1.4948539

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OCA

[1] Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN Jr. Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. Struct Dyn. 2016 Apr 29;3(3):034702. doi: 10.1063/1.4948539. eCollection 2016, May. PMID:27191010 doi:https://dx.doi.org/10.1063/1.4948539

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='4q31' size='340' side='right'caption='[[4q31]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4q31]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_15837 Atcc 15837]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q31 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q31 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4q31]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_echinospora Micromonospora echinospora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q31 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 2.099&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">calE6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1877 ATCC 15837])</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=4q31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q31 OCA], [https://pdbe.org/4q31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q31 RCSB], [https://www.ebi.ac.uk/pdbsum/4q31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q31 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=4q31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q31 OCA], [http://pdbe.org/4q31 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q31 RCSB], [http://www.ebi.ac.uk/pdbsum/4q31 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q31 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8KNG3_MICEC Q8KNG3_MICEC]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 15837]]
 [[Category: Large Structures]]
-[[Category: Babnigg, G]]
+[[Category: Micromonospora echinospora]]
-[[Category: Bigelow, L]]
+[[Category: Babnigg G]]
-[[Category: Bingman, C A]]
+[[Category: Bigelow L]]
-[[Category: Jedrzejczak, R]]
+[[Category: Bingman CA]]
-[[Category: Joachimiak, A]]
+[[Category: Jedrzejczak R]]
-[[Category: Kharel, M K]]
+[[Category: Joachimiak A]]
-[[Category: Structural genomic]]
+[[Category: Kharel MK]]
-[[Category: NatPro, Enzyme Discovery for Natural Product Biosynthesis]]
+[[Category: Phillips Jr GN]]
-[[Category: Phillips, G N]]
+[[Category: Singh S]]
-[[Category: Singh, S]]
+[[Category: Tan K]]
-[[Category: Tan, K]]
+[[Category: Thorson JS]]
-[[Category: Thorson, J S]]
+[[Category: Yennamalli RM]]
-[[Category: Yennamalli, R M]]
-[[Category: Enzyme discovery for natural product biosynthesis]]
-[[Category: Lyase]]
-[[Category: Mcsg]]
-[[Category: Natpro]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Psi-biology]]

4q31: Difference between revisions

Latest revision as of 23:05, 26 March 2025

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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