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| | ==Crystal structure of ntda from bacillus subtilis with bound cofactor pmp== | | ==Crystal structure of ntda from bacillus subtilis with bound cofactor pmp== |
| - | <StructureSection load='4k2i' size='340' side='right' caption='[[4k2i]], [[Resolution|resolution]] 2.23Å' scene=''> | + | <StructureSection load='4k2i' size='340' side='right'caption='[[4k2i]], [[Resolution|resolution]] 2.23Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4k2i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K2I FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k2i]] 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=4K2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K2I FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr> | + | </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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k2b|4k2b]], [[4k2m|4k2m]]</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=4k2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k2i OCA], [https://pdbe.org/4k2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k2i RCSB], [https://www.ebi.ac.uk/pdbsum/4k2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k2i ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">939788, BSU10550, NP_388936.1, ntdA, yhjL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
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| - | <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=4k2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k2i OCA], [http://pdbe.org/4k2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k2i RCSB], [http://www.ebi.ac.uk/pdbsum/4k2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k2i ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Palmer, D R.J]]
| + | [[Category: Large Structures]] |
| - | [[Category: Sanders, D A.R]]
| + | [[Category: Palmer DRJ]] |
| - | [[Category: Straaten, K E.Van]] | + | [[Category: Sanders DAR]] |
| - | [[Category: Additional n-terninal domain]] | + | [[Category: Van Straaten KE]] |
| - | [[Category: Aspertate aminotransferase fold]] | + | |
| - | [[Category: Homo-dimer]] | + | |
| - | [[Category: Sugar aminotransferase]]
| + | |
| - | [[Category: Transferase]]
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| Structural highlights
Function
NTDA_BACSU Part of the ntdABC operon that biosynthesizes the NTD (3,3'-neotrehalosadiamine) antibiotic.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ van Straaten KE, Ko JB, Jagdhane R, Anjum S, Palmer DR, Sanders DA. The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new sub-class of aminotransferases. J Biol Chem. 2013 Oct 4. PMID:24097983 doi:http://dx.doi.org/10.1074/jbc.M113.500637
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