4fwi: Difference between revisions

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 ==Crystal structure of the nucleotide-binding domain of a dipeptide ABC transporter==
-<StructureSection load='4fwi' size='340' side='right' caption='[[4fwi]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
+<StructureSection load='4fwi' size='340' side='right'caption='[[4fwi]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fwi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FWI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FWI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fwi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FWI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.892&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DppD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273068 Caldanaerobacter subterraneus subsp. tengcongensis])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=4fwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwi OCA], [http://pdbe.org/4fwi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fwi RCSB], [http://www.ebi.ac.uk/pdbsum/4fwi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fwi 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=4fwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwi OCA], [https://pdbe.org/4fwi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fwi RCSB], [https://www.ebi.ac.uk/pdbsum/4fwi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fwi ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/DPPD_CALS4 DPPD_CALS4] Part of the ABC transporter Dpp involved in dipeptide transport. Responsible for energy coupling to the transport system.[UniProtKB:A2RI77]
-Dipeptide permease (Dpp), which belongs to an ABC transport system, imports peptides consisting of two or three L-amino acids from the matrix to the cytoplasm in microbes. Previous studies have indicated that haem competes with dipeptides to bind DppA in vitro and in vivo and that the Dpp system can also translocate haem. Here, the crystal structure of DppD, the nucleotide-binding domain (NBD) of the ABC-type dipeptide/oligopeptide/nickel-transport system from Thermoanaerobacter tengcongensis, bound with ATP, Mg(2+) and a [4Fe-4S] iron-sulfur cluster is reported. The N-terminal domain of DppD shares a similar structural fold with the NBDs of other ABC transporters. Interestingly, the C-terminal domain of DppD contains a [4Fe-4S] cluster. The UV-visible absorbance spectrum of DppD was consistent with the presence of a [4Fe-4S] cluster. A search with DALI revealed that the [4Fe-4S] cluster-binding domain is a novel structural fold. Structural analysis and comparisons with other ABC transporters revealed that this iron-sulfur cluster may act as a mediator in substrate (dipeptide or haem) binding by electron transfer and may regulate the transport process in Dpp ABC transport systems. The crystal structure provides a basis for understanding the properties of ABC transporters and will be helpful in investigating the functions of NBDs in the regulation of ABC transporter activity.
-Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.,Li X, Zhuo W, Yu J, Ge J, Gu J, Feng Y, Yang M, Wang L, Wang N Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):256-65. doi:, 10.1107/S0907444912045180. Epub 2013 Jan 19. PMID:23385461<ref>PMID:23385461</ref>
+==See Also==
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4fwi" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
+[[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]]
-[[Category: Ge, J]]
+[[Category: Large Structures]]
-[[Category: Li, X]]
+[[Category: Ge J]]
-[[Category: Wang, N]]
+[[Category: Li X]]
-[[Category: Yang, M]]
+[[Category: Wang N]]
-[[Category: Abc transporter]]
+[[Category: Yang M]]
-[[Category: Iron-sulfur cluster]]
-[[Category: Nbd]]
-[[Category: Nucleotide binding]]
-[[Category: Transport protein]]