6l1n

From Proteopedia

(Difference between revisions)

Current revision

Substrate bound BacF structure from Bacillus subtillis

Structural highlights

6l1n is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BACF_BACSU Part of the bacABCDEF operon responsible for the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. Bacilysin is an irreversible inactivator of the glutaminase domain of glucosamine synthetase (PubMed:20052993). Catalyzes the reductive amination of the C2 ketone of tetrahydro-hydroxyphenylpyruvate (H4HPP), with L-Phe as an amino donor, to yield tetrahydrotyrosine (H4Tyr) diastereomer (PubMed:22765234). D-Phe is not an effective amino donor (PubMed:22765234). BacF associated to BacG converts 3E,7R- and 3Z,7R-ex-H2HPP to 2S,4R,7R- and 2S,4S,7R-H4Tyr, respectively. Given that bacilysin has the 2S,4S stereochemistry in its anticapsin moiety, it is likely that the 2S,4S-H4Tyr is the diastereomer used for the biosynthesis (PubMed:22765234).^[1] ^[2]

Publication Abstract from PubMed

The nonribosomal biosynthesis of the dipeptide antibiotic bacilysin is achieved by the concerted action of multiple enzymes in the Bacillus subtilis bac operon. BacF (YwfG), encoded by the bacF gene, is a fold type I pyridoxal 5-phosphate (PLP)-dependent stereospecific transaminase. Activity assays with L-phenylalanine and 4-hydroxyphenylpyruvic acid (4HPP), a chemical analogue of tetrahydrohydroxyphenylpyruvic acid (H4HPP), revealed stereospecific substrate preferences, a finding that was consistent with previous reports on the role of this enzyme in bacilysin synthesis. The crystal structure of this dimeric enzyme was determined in its apo form as well as in substrate-bound and product-bound conformations. Two ligand-bound structures were determined by soaking BacF crystals with substrates (L-phenylalanine and 4-hydroxyphenylpyruvate). These structures reveal multiple catalytic steps: the internal aldimine with PLP and two external aldimine conformations that show the rearrangement of the external aldimine to generate product (L-tyrosine). Together, these structural snapshots provide an insight into the catalytic mechanism of this transaminase.

Structural insights into the catalytic mechanism of Bacillus subtilis BacF.,Deshmukh A, Gopal B Acta Crystallogr F Struct Biol Commun. 2020 Mar 1;76(Pt 3):145-151. doi:, 10.1107/S2053230X20001636. Epub 2020 Mar 3. PMID:32134000^[3]

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

References

↑ Mahlstedt SA, Walsh CT. Investigation of anticapsin biosynthesis reveals a four-enzyme pathway to tetrahydrotyrosine in Bacillus subtilis. Biochemistry. 2010 Feb 9;49(5):912-23. PMID:20052993 doi:10.1021/bi9021186
↑ Parker JB, Walsh CT. Stereochemical outcome at four stereogenic centers during conversion of prephenate to tetrahydrotyrosine by BacABGF in the bacilysin pathway. Biochemistry. 2012 Jul 17;51(28):5622-32. PMID:22765234 doi:10.1021/bi3006362
↑ Deshmukh A, Gopal B. Structural insights into the catalytic mechanism of Bacillus subtilis BacF. Acta Crystallogr F Struct Biol Commun. 2020 Mar 1;76(Pt 3):145-151. doi:, 10.1107/S2053230X20001636. Epub 2020 Mar 3. PMID:32134000 doi:http://dx.doi.org/10.1107/S2053230X20001636

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6l1n"

Categories: Bacillus subtilis | Large Structures | Balasubramanian G | Deshmukh AA

@@ Line 3: / Line 3: @@
 <StructureSection load='6l1n' size='340' side='right'caption='[[6l1n]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6l1n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L1N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6l1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L1N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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&#8491;</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=6l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l1n OCA], [http://pdbe.org/6l1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l1n RCSB], [http://www.ebi.ac.uk/pdbsum/6l1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l1n ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=6l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l1n OCA], [https://pdbe.org/6l1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l1n RCSB], [https://www.ebi.ac.uk/pdbsum/6l1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l1n ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/BACF_BACSU BACF_BACSU] Part of the bacABCDEF operon responsible for the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. Bacilysin is an irreversible inactivator of the glutaminase domain of glucosamine synthetase (PubMed:20052993). Catalyzes the reductive amination of the C2 ketone of tetrahydro-hydroxyphenylpyruvate (H4HPP), with L-Phe as an amino donor, to yield tetrahydrotyrosine (H4Tyr) diastereomer (PubMed:22765234). D-Phe is not an effective amino donor (PubMed:22765234). BacF associated to BacG converts 3E,7R- and 3Z,7R-ex-H2HPP to 2S,4R,7R- and 2S,4S,7R-H4Tyr, respectively. Given that bacilysin has the 2S,4S stereochemistry in its anticapsin moiety, it is likely that the 2S,4S-H4Tyr is the diastereomer used for the biosynthesis (PubMed:22765234).<ref>PMID:20052993</ref> <ref>PMID:22765234</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 19: @@
 </div>
 <div class="pdbe-citations 6l1n" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Balasubramanian, G]]
+[[Category: Balasubramanian G]]
-[[Category: Deshmukh, A A]]
+[[Category: Deshmukh AA]]
-[[Category: Aminotransferase]]
-[[Category: Plp dependent enzyme]]
-[[Category: Transferase]]

6l1n

From Proteopedia

Current revision

Substrate bound BacF structure from Bacillus subtillis

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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