4k2m
From Proteopedia
(Difference between revisions)
| (One intermediate revision not shown.) | |||
| Line 4: | Line 4: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4k2m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K2M FirstGlance]. <br> | <table><tr><td colspan='2'>[[4k2m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K2M FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=O1G:3-DEOXY-3-[(E)-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)AMINO]-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>O1G</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]] 1.71Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=O1G:3-DEOXY-3-[(E)-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)AMINO]-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE'>O1G</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=4k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k2m OCA], [https://pdbe.org/4k2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k2m RCSB], [https://www.ebi.ac.uk/pdbsum/4k2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k2m ProSAT]</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=4k2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k2m OCA], [https://pdbe.org/4k2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k2m RCSB], [https://www.ebi.ac.uk/pdbsum/4k2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k2m ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/NTDA_BACSU NTDA_BACSU] Part of the ntdABC operon that biosynthesizes the NTD (3,3'-neotrehalosadiamine) antibiotic. | [https://www.uniprot.org/uniprot/NTDA_BACSU NTDA_BACSU] Part of the ntdABC operon that biosynthesizes the NTD (3,3'-neotrehalosadiamine) antibiotic. | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | NtdA from Bacillus subtilis is a sugar aminotransferase (SAT) that catalyses the PLP-dependent equatorial transamination of 3-oxo-alpha-D-glucose-6-phosphate to form alpha-D-kanosamine-6-phosphate. The crystal structure of NtdA shows that NtdA shares the common aspartate aminotransferase fold (AAT Type 1) with residues from both monomers forming the active site. The crystal structures of NtdA alone, co-crystallized with the product alpha-D-kanosamine-6-phosphate and incubated with the amine donor glutamate reveals three key structures in the mechanistic pathway of NtdA. The structure of NtdA alone reveals the internal aldimine form of NtdA with the cofactor PLP covalently attached to Lys247. Addition of glutamate results in formation of pyridoxamine phosphate. Co-crystallization with kanosamine-6-phosphate results in the formation of the external aldimine. Only alpha-D-kanosamine-6-phosphate is observed in the active site of NtdA, not the beta-anomer. A comparison of the structure and sequence of NtdA with other SATs enables us to propose that the VIbeta family of aminotransferases should be divided into subfamilies based on the catalytic lysine motif. | ||
| - | |||
| - | The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new sub-class of aminotransferases.,van Straaten KE, Ko JB, Jagdhane R, Anjum S, Palmer DR, Sanders DA J Biol Chem. 2013 Oct 4. PMID:24097983<ref>PMID:24097983</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4k2m" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal structure of ntda from bacillus subtilis in complex with the plp external aldimine adduct with kanosamine-6-phosphate
| |||||||||||
