View source for 4xfm


==Crystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, with bound D-threonate, domain swapped dimer==
<StructureSection load='4xfm' size='340' side='right'caption='[[4xfm]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4xfm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pectobacterium_atrosepticum_SCRI1043 Pectobacterium atrosepticum SCRI1043]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XFM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THE:THREONATE+ION'>THE</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=4xfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xfm OCA], [https://pdbe.org/4xfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xfm RCSB], [https://www.ebi.ac.uk/pdbsum/4xfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xfm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DTNK_PECAS DTNK_PECAS] Catalyzes the ATP-dependent phosphorylation of D-threonate to D-threonate 4-phosphate. Can also phosphorylate 4-hydroxy-L-threonine, with lower efficiency.<ref>PMID:27402745</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using a large-scale "genomic enzymology" approach, we (i) assigned novel ATP-dependent four-carbon acid sugar kinase functions to members of the DUF1537 protein family (domain of unknown function; Pfam families PF07005 and PF17042) and (ii) discovered novel catabolic pathways for d-threonate, l-threonate, and d-erythronate. The experimentally determined ligand specificities of several solute binding proteins (SBPs) for TRAP (tripartite ATP-independent permease) transporters for four-carbon acids, including d-erythronate and l-erythronate, were used to constrain the substrates for the catabolic pathways that degrade the SBP ligands to intermediates in central carbon metabolism. Sequence similarity networks and genome neighborhood networks were used to identify the enzyme components of the pathways. Conserved genome neighborhoods encoded SBPs as well as permease components of the TRAP transporters, members of the DUF1537 family, and a member of the 4-hydroxy-l-threonine 4-phosphate dehydrogenase (PdxA) oxidative decarboxylase, class II aldolase, or ribulose 1,5-bisphosphate carboxylase/oxygenase, large subunit (RuBisCO) superfamily. Because the characterized substrates of members of the PdxA, class II aldolase, and RuBisCO superfamilies are phosphorylated, we postulated that the members of the DUF1537 family are novel ATP-dependent kinases that participate in catabolic pathways for four-carbon acid sugars. We determined that (i) the DUF1537/PdxA pair participates in a pathway for the conversion of d-threonate to dihydroxyacetone phosphate and CO2 and (ii) the DUF1537/class II aldolase pair participates in pathways for the conversion of d-erythronate and l-threonate (epimers at carbon-3) to dihydroxyacetone phosphate and CO2 The physiological importance of these pathways was demonstrated in vivo by phenotypic and genetic analyses.

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.,Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crecy-Lagard V, Jacobson MP, Almo SC, Gerlt JA Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4161-9. doi:, 10.1073/pnas.1605546113. Epub 2016 Jul 11. PMID:27402745<ref>PMID:27402745</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4xfm" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pectobacterium atrosepticum SCRI1043]]
[[Category: Al Obaidi NF]]
[[Category: Almo SC]]
[[Category: Attonito JD]]
[[Category: Benach J]]
[[Category: Chamala S]]
[[Category: Chowdhury S]]
[[Category: Gerlt JA]]
[[Category: Lafleur J]]
[[Category: Love J]]
[[Category: Morisco LL]]
[[Category: Scott Glenn A]]
[[Category: Seidel RD]]
[[Category: Toro R]]
[[Category: Vetting MW]]
[[Category: Wasserman SR]]
[[Category: Whalen KL]]