This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2hzk

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 00:28, 11 September 2015

Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its open form

Structural highlights

2hzk is a 4 chain structure with sequence from Rhos4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[TAKP_RHOS4] Part of the tripartite ATP-independent periplasmic (TRAP) transport system TakPQM involved in the uptake of alpha-keto acids. This protein specifically binds alpha-keto acids including pyruvate, oxobutyrate, oxovalerate and 4-methyl-2-oxovalerate. Ligand-binding affinity increases with the increasing chain length of the aliphatic backbone of the ligand. Is not able to bind alpha-ketoglutarate.[UniProtKB:P44542]^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

BACKGROUND: The import of solutes into the bacterial cytoplasm involves several types of membrane transporters, which may be driven by ATP hydrolysis (ABC transporters) or by an ion or H+ electrochemical membrane potential, as in the tripartite ATP-independent periplasmic system (TRAP). In both the ABC and TRAP systems, a specific periplasmic protein from the ESR family (Extracytoplasmic Solute Receptors) is often involved for the recruitment of the solute and its presentation to the membrane complex. In Rhodobacter sphaeroides, TakP (previously named SmoM) is an ESR from a TRAP transporter and binds alpha-keto acids in vitro. RESULTS: We describe the high-resolution crystal structures of TakP in its unliganded form and as a complex with sodium-pyruvate. The results show a limited "Venus flytrap" conformational change induced by substrate binding. In the liganded structure, a cation (most probably a sodium ion) is present and plays a key role in the association of the pyruvate to the protein. The structure of the binding pocket gives a rationale for the relative affinities of various ligands that were tested from a fluorescence assay. The protein appears to be dimeric in solution and in the crystals, with a helix-swapping structure largely participating in the dimer formation. A 30 A-long water channel buried at the dimer interface connects the two ligand binding cavities of the dimer. CONCLUSION: The concerted recruitment by TakP of the substrate group with a cation could represent a first step in the coupled transport of both partners, providing the driving force for solute import. Furthermore, the unexpected dimeric structure of TakP suggests a molecular mechanism of solute uptake by the dimeric ESR via a channel that connects the binding sites of the two monomers.

Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.,Gonin S, Arnoux P, Pierru B, Lavergne J, Alonso B, Sabaty M, Pignol D BMC Struct Biol. 2007 Mar 15;7:11. PMID:17362499^[2]

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

References

↑ Gonin S, Arnoux P, Pierru B, Lavergne J, Alonso B, Sabaty M, Pignol D. Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding. BMC Struct Biol. 2007 Mar 15;7:11. PMID:17362499 doi:10.1186/1472-6807-7-11
↑ Gonin S, Arnoux P, Pierru B, Lavergne J, Alonso B, Sabaty M, Pignol D. Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding. BMC Struct Biol. 2007 Mar 15;7:11. PMID:17362499 doi:10.1186/1472-6807-7-11

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2hzk"

@@ Line 2: / Line 2: @@
 <StructureSection load='2hzk' size='340' side='right' caption='[[2hzk]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2hzk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides_2.4.1 Rhodobacter sphaeroides 2.4.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HZK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2hzk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhos4 Rhos4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HZK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HZK FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2hzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hzk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hzk RCSB], [http://www.ebi.ac.uk/pdbsum/2hzk PDBsum]</span></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=2hzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hzk OCA], [http://pdbe.org/2hzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hzk RCSB], [http://www.ebi.ac.uk/pdbsum/2hzk PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/TAKP_RHOS4 TAKP_RHOS4]] Part of the tripartite ATP-independent periplasmic (TRAP) transport system TakPQM involved in the uptake of alpha-keto acids. This protein specifically binds alpha-keto acids including pyruvate, oxobutyrate, oxovalerate and 4-methyl-2-oxovalerate. Ligand-binding affinity increases with the increasing chain length of the aliphatic backbone of the ligand. Is not able to bind alpha-ketoglutarate.[UniProtKB:P44542]<ref>PMID:17362499</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2hzk" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Rhodobacter sphaeroides 2 4.1]]
+[[Category: Rhos4]]
 [[Category: Alonso, B]]
 [[Category: Arnoux, P]]

2hzk

From Proteopedia

Revision as of 00:28, 11 September 2015

Crystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its open form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox