6af6: Difference between revisions

Latest revision as of 09:28, 22 November 2023

PigA with FAD and proline

Structural highlights

6af6 is a 1 chain structure with sequence from Serratia sp. ATCC 39006. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.62Å
Ligands:	CL, FAD, GLY, O4B, PRO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PIGA_SERS3 Involved in the biosynthesis of 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC), one of the terminal products involved in the biosynthesis of the red antibiotic prodigiosin (Pig). Catalyzes the desaturation of the L-prolyl-[PigG] to yield 1H-pyrrole-2-carbonyl-[PigG].^[1] ^[2]

Publication Abstract from PubMed

Prodigiosin is an intensely red pigment comprising three pyrroles. The biosynthetic pathway includes a two-step proline oxidation catalyzed by PigA, using FAD as its cofactor. Here the enzyme is crystallized in apo-form and in complex with FAD and proline. As an acyl-CoA dehydrogenase (ACAD) family member, the protein folds into a beta-sheet flanked by two alpha-helical domains. PigA forms a tetramer, consistent with analytical ultracentrifugation results. FAD binds to PigA in a similar way to that in the other ACAD-family enzymes. The variable conformations of loop beta4-beta5 and helix alphaG correlate well with the structural flexibility required for substrate entrance to the Re side of FAD. Modeling with PigG, the acyl carrier protein, suggests a reasonable mode of interaction with PigA. The structure helps explain the proline oxidation mechanism, in which Glu244 plays a central role by abstracting the substrate protons. It also reveals a plausible pocket for oxygen binding to the Si side of FAD.

Crystal structure of PigA, a prolyl thioester-oxidizing enzyme in prodigiosin biosynthesis.,Lee CC, Ko TP, Chen CT, Chan YT, Lo SY, Chang JY, Chen YW, Chung TF, Hsieh HJ, Hsiao CD, Wang AH Chembiochem. 2018 Aug 10. doi: 10.1002/cbic.201800409. PMID:30095206^[3]

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

References

↑ Williamson NR, Simonsen HT, Ahmed RA, Goldet G, Slater H, Woodley L, Leeper FJ, Salmond GP. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol Microbiol. 2005 May;56(4):971-89. PMID:15853884 doi:https://dx.doi.org/10.1111/j.1365-2958.2005.04602.x
↑ Garneau-Tsodikova S, Dorrestein PC, Kelleher NL, Walsh CT. Protein assembly line components in prodigiosin biosynthesis: characterization of PigA,G,H,I,J. J Am Chem Soc. 2006 Oct 4;128(39):12600-1. PMID:17002325 doi:https://dx.doi.org/10.1021/ja063611l
↑ Lee CC, Ko TP, Chen CT, Chan YT, Lo SY, Chang JY, Chen YW, Chung TF, Hsieh HJ, Hsiao CD, Wang AH. Crystal structure of PigA, a prolyl thioester-oxidizing enzyme in prodigiosin biosynthesis. Chembiochem. 2018 Aug 10. doi: 10.1002/cbic.201800409. PMID:30095206 doi:https://dx.doi.org/10.1002/cbic.201800409

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Williamson NR, Simonsen HT, Ahmed RA, Goldet G, Slater H, Woodley L, Leeper FJ, Salmond GP. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol Microbiol. 2005 May;56(4):971-89. PMID:15853884 doi:https://dx.doi.org/10.1111/j.1365-2958.2005.04602.x

[2] Garneau-Tsodikova S, Dorrestein PC, Kelleher NL, Walsh CT. Protein assembly line components in prodigiosin biosynthesis: characterization of PigA,G,H,I,J. J Am Chem Soc. 2006 Oct 4;128(39):12600-1. PMID:17002325 doi:https://dx.doi.org/10.1021/ja063611l

[3] Lee CC, Ko TP, Chen CT, Chan YT, Lo SY, Chang JY, Chen YW, Chung TF, Hsieh HJ, Hsiao CD, Wang AH. Crystal structure of PigA, a prolyl thioester-oxidizing enzyme in prodigiosin biosynthesis. Chembiochem. 2018 Aug 10. doi: 10.1002/cbic.201800409. PMID:30095206 doi:https://dx.doi.org/10.1002/cbic.201800409

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='6af6' size='340' side='right'caption='[[6af6]], [[Resolution|resolution]] 1.62&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6af6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sers3 Sers3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AF6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AF6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6af6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_sp._ATCC_39006 Serratia sp. ATCC 39006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AF6 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=O4B:1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE'>O4B</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</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]] 1.62&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5zw0|5zw0]], [[5zw2|5zw2]], [[5zw7|5zw7]], [[5zw8|5zw8]]</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=O4B:1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE'>O4B</scene>, <scene name='pdbligand=PRO:PROLINE'>PRO</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pigA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=104623 SERS3])</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=6af6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6af6 OCA], [https://pdbe.org/6af6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6af6 RCSB], [https://www.ebi.ac.uk/pdbsum/6af6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6af6 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-prolyl-[peptidyl-carrier_protein]_dehydrogenase L-prolyl-[peptidyl-carrier protein] dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.14 1.3.8.14] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6af6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6af6 OCA], [http://pdbe.org/6af6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6af6 RCSB], [http://www.ebi.ac.uk/pdbsum/6af6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6af6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PIGA_SERS3 PIGA_SERS3]] Involved in the biosynthesis of 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC), one of the terminal products involved in the biosynthesis of the red antibiotic prodigiosin (Pig). Catalyzes the desaturation of the L-prolyl-[PigG] to yield 1H-pyrrole-2-carbonyl-[PigG].<ref>PMID:15853884</ref> <ref>PMID:17002325</ref>
+[https://www.uniprot.org/uniprot/PIGA_SERS3 PIGA_SERS3] Involved in the biosynthesis of 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC), one of the terminal products involved in the biosynthesis of the red antibiotic prodigiosin (Pig). Catalyzes the desaturation of the L-prolyl-[PigG] to yield 1H-pyrrole-2-carbonyl-[PigG].<ref>PMID:15853884</ref> <ref>PMID:17002325</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Sers3]]
+[[Category: Serratia sp. ATCC 39006]]
-[[Category: Ko, T P]]
+[[Category: Ko T-P]]
-[[Category: Lee, C C]]
+[[Category: Lee C-C]]
-[[Category: Wang, A H.J]]
+[[Category: Wang AHJ]]
-[[Category: Acyl-coa oxidase]]
-[[Category: Biosynthetic protein]]
-[[Category: Fad]]
-[[Category: Pyrrole]]
-[[Category: Red pigment]]
-[[Category: Tetramer]]

6af6: Difference between revisions

Latest revision as of 09:28, 22 November 2023

PigA with FAD and proline

Structural highlights

Function

Publication Abstract from PubMed

References

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