Mycobacterium tuberculosis ArfA Rv0899: Difference between revisions

The Rv0899 ArfA protein [[http://www.uniprot.org/uniprot/P9WIU5 ARFA_MYCTU]] from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] belongs to the OmpA (outer membrane protein A) family of outer membrane proteins and has been proposed to act as an outer membrane [[porin]] with ion channel activity and contributes to the bacterium's adaptation to the acidic environment in phagosome [http://en.wikipedia.org/wiki/Phagosome] during infection <ref>PMID: 21117233 </ref>. Rv0899 protein encoded by an ammonia release facilator operon that is necessary for rapid ammonia secretion, pH neutralization and adaptation to acidic environments in vitro. Two M. tuberculosis H37Rv genes (Rv0900 [[http://www.uniprot.org/uniprot/P9WJG7 ARFB_MYCTU]] and Rv0901 [[http://www.uniprot.org/uniprot/P9WJG5 ARFC_MYCTU]] ) adjacent to Rv0899 also encode putative membrane proteins, and are found exclusively in association with Rv0899 in the same pathogenic mycobacteria, suggesting that the three may constitute an operon dedicated to a common function.

Asparagine is the primary ammonia source for Mycobacterium tuberculosis H37Rv at acidic pH <ref>PMID: 21410778 </ref>.

The deletion of this gene impairs the uptake of some water-soluble substances, such as serine, glucose, and glycerol <ref>PMID: 12366842 </ref>.

 

<table><tr><td colspan='2'>[[2l26]] is a 1 chain structure with sequence from ''Mycobacterium tuberculosis''. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L26 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2L26 FirstGlance]. <br>

</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=2l26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l26 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2l26 RCSB], [http://www.ebi.ac.uk/pdbsum/2l26 PDBsum]</span></td></tr>

The central B domain (<scene name='61/612805/Secondary_structure_b/1'>residues 73-200</scene>> folds </scene> with three parallel/antiparallel alpha-{{Template:ColorKey_helixes}} packed against six parallel/antiparallel beta-{{Template:ColorKey_strands}} that form a flat beta-sheet. The B domain has homology with conserved putative <scene name='61/612805/Conserved_g95_and_g164_in_bon/2'>lipid-binding BON</scene> (bacterial OsmY and nodulation) superfamily domains  and conserved Gly95 and Gly164 [http://www.ebi.ac.uk/interpro/entry/IPR014004]. <scene name='61/612805/Surface2/1'>The core</scene> is {{Template:ColorKey_Hydrophobic}}, while the exterior is {{Template:ColorKey_Polar}} and predominantly acidic. The two subdomains are symmetric about α2, and their backbone atoms can be aligned with a RMSD [http://http://en.wikipedia.org/wiki/Root-mean-square_deviation] of 1.8Å, by performing a 180° rotation of either one around an axis normal to the 6-stranded β-sheet.

The C domain <scene name='61/612805/C_domain/1'>(residues 201-326)</scene> has homology to the OmpA-C-like superfamily of periplasmic peptidoglycan-binding sequences, found in several types of bacterial membrane proteins.The C domain of wild-type ArfA <scene name='61/612805/C_domain/3'></scene> <scene name='61/612805/C_domain_1/1'> folds </scene> into four β-strands and four α-helices.Three parallel (β1, β2, β3) and one antiparallel (β4) β-strands form a four-stranded β-sheet (β1–β4-β2–β3) that packs against three α-helices (α1, α2, α3), while a fourth helix (α4) extends from the N-terminus of β4. The structure <scene name='61/612805/C_domain_stabilization/2'> is stabilized </scene> by disulfide bond between C208 and C250, by a network of hydrophobic contacts between α1, α2 and β4 (L211, I215, V243, L247, Ile323 and V325) between side chains and by a hydrogen bond between the backbone amide of V325 and the side-chain carbonyl of Q212.  

1. Acquisition of Zn(2+) ions.

Using [[NMR]] chemical shift perturbation and isothermal calorimetric titration assays, Rv0899 was able to interact with <scene name='61/612805/Binding-site_for_zn/1'>Zn(2+) ions</scene>, which may indicate a role for Rv0899 in the process of Zn(2+) acquisition.

<ref>PMID: 22108166 </ref>

2. Bacterium's adaptation to the acidic environment of the phagosome during infection.

The amino acid pair <scene name='61/612805/Asn111_and_gly112/1'> Asn111-Gly112 </scene>, located at the end of α1 and preceding L3, undergoes in-vitro deamidation, a pH-dependent reaction whereby Asn is converted to Asp and ammonia is released. Asparagine residues preceding glycine, and situated in conformationally flexible regions of proteins, are frequently deamidated, with potentially significant consequences for protein regulation and function. In the case of Rv0899, deamidation and the concomitant release of ammonia could have important consequences for the acid adaptation function of the protein. <ref>PMID: 20199110</ref>

  [[Image:Asparaginase-reaction.jpg|250px]]

It exhibits pH-dependent conformational dynamics 232, 225, 240, 244, 281, 285 <scene name='61/612805/D236_before_mutation/1'>in neutral pH (D236) </scene> and a more ordered structure at <scene name='61/612805/D236a_after_mut/3'>acidic pH (D236A) </scene>, which could be related to its acid stress response.

==Localization in membrane==