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==Structural Genomics, RpiB/AlsB==
==Structural Genomics, RpiB/AlsB==
<StructureSection load='1nn4' size='340' side='right' caption='[[1nn4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1nn4' size='340' side='right'caption='[[1nn4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1nn4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NN4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1nn4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NN4 FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPIB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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]] 2.2&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribose-5-phosphate_isomerase Ribose-5-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.6 5.3.1.6] </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=1nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nn4 OCA], [https://pdbe.org/1nn4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nn4 RCSB], [https://www.ebi.ac.uk/pdbsum/1nn4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nn4 ProSAT], [https://www.topsan.org/Proteins/MCSG/1nn4 TOPSAN]</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=1nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nn4 OCA], [http://pdbe.org/1nn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nn4 RCSB], [http://www.ebi.ac.uk/pdbsum/1nn4 PDBsum], [http://www.topsan.org/Proteins/MCSG/1nn4 TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RPIB_ECOLI RPIB_ECOLI]] In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate.<ref>PMID:8576032</ref> <ref>PMID:4909663</ref> <ref>PMID:1104357</ref> <ref>PMID:9401019</ref> <ref>PMID:18640127</ref>
[https://www.uniprot.org/uniprot/RPIB_ECOLI RPIB_ECOLI] In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate.<ref>PMID:8576032</ref> <ref>PMID:4909663</ref> <ref>PMID:1104357</ref> <ref>PMID:9401019</ref> <ref>PMID:18640127</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nn/1nn4_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nn/1nn4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 19: Line 19:
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nn4 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nn4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribose-5-phosphate isomerases (EC 5.3.1.6) interconvert ribose 5-phosphate and ribulose 5-phosphate. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated types of enzyme can catalyze the reaction. The most common, RpiA, is present in almost all organisms (including Escherichia coli), and is highly conserved. The second type, RpiB, is present in some bacterial and eukaryotic species and is well conserved. In E.coli, RpiB is sometimes referred to as AlsB, because it can take part in the metabolism of the rare sugar, allose, as well as the much more common ribose sugars. We report here the structure of RpiB/AlsB from E.coli, solved by multi-wavelength anomalous diffraction (MAD) phasing, and refined to 2.2A resolution. RpiB is the first structure to be solved from pfam02502 (the RpiB/LacAB family). It exhibits a Rossmann-type alphabetaalpha-sandwich fold that is common to many nucleotide-binding proteins, as well as other proteins with different functions. This structure is quite distinct from that of the previously solved RpiA; although both are, to some extent, based on the Rossmann fold, their tertiary and quaternary structures are very different. The four molecules in the RpiB asymmetric unit represent a dimer of dimers. Active-site residues were identified at the interface between the subunits, such that each active site has contributions from both subunits. Kinetic studies indicate that RpiB is nearly as efficient as RpiA, despite its completely different catalytic machinery. The sequence and structural results further suggest that the two homologous components of LacAB (galactose-6-phosphate isomerase) will compose a bi-functional enzyme; the second activity is unknown.
The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction.,Zhang RG, Andersson CE, Skarina T, Evdokimova E, Edwards AM, Joachimiak A, Savchenko A, Mowbray SL J Mol Biol. 2003 Oct 3;332(5):1083-94. PMID:14499611<ref>PMID:14499611</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1nn4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribose-5-phosphate isomerase|Ribose-5-phosphate isomerase]]
*[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Ribose-5-phosphate isomerase]]
[[Category: Large Structures]]
[[Category: Andersson, C E]]
[[Category: Andersson CE]]
[[Category: Arrowsmith, C]]
[[Category: Arrowsmith C]]
[[Category: Beasley, S L]]
[[Category: Beasley SL]]
[[Category: Edwards, A M]]
[[Category: Edwards AM]]
[[Category: Evdokimova, E]]
[[Category: Evdokimova E]]
[[Category: Joachimiak, A]]
[[Category: Joachimiak A]]
[[Category: Structural genomic]]
[[Category: Mowbray SL]]
[[Category: Mowbray, S L]]
[[Category: Savchenko A]]
[[Category: Savchenko, A]]
[[Category: Skarina T]]
[[Category: Skarina, T]]
[[Category: Zhang RG]]
[[Category: Zhang, R G]]
[[Category: Alpha/beta/alpha sandwich]]
[[Category: Isomerase]]
[[Category: Mcsg]]
[[Category: PSI, Protein structure initiative]]

Latest revision as of 10:57, 14 February 2024

Structural Genomics, RpiB/AlsBStructural Genomics, RpiB/AlsB

Structural highlights

1nn4 is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

RPIB_ECOLI In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate.[1] [2] [3] [4] [5]

Evolutionary Conservation

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

See Also

References

  1. ↑ Sorensen KI, Hove-Jensen B. Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression. J Bacteriol. 1996 Feb;178(4):1003-11. PMID:8576032
  2. ↑ David J, Wiesmeyer H. Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities. Biochim Biophys Acta. 1970 Apr 14;208(1):56-67. PMID:4909663
  3. ↑ Essenberg MK, Cooper RA. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. Eur J Biochem. 1975 Jul 1;55(2):323-32. PMID:1104357
  4. ↑ Kim C, Song S, Park C. The D-allose operon of Escherichia coli K-12. J Bacteriol. 1997 Dec;179(24):7631-7. PMID:9401019
  5. ↑ Roos AK, Mariano S, Kowalinski E, Salmon L, Mowbray SL. D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not. J Mol Biol. 2008 Oct 10;382(3):667-79. Epub 2008 Jul 9. PMID:18640127 doi:10.1016/j.jmb.2008.06.090

1nn4, resolution 2.20Å

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