1qd9

From Proteopedia

(Difference between revisions)

Revision as of 09:54, 15 September 2021

Bacillus subtilis YABJ

Structural highlights

1qd9 is a 3 chain structure with sequence from "vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RIDA_BACSU] Accelerates the release of ammonia from reactive enamine/imine intermediates of the PLP-dependent threonine dehydratase (IlvA) in the low water environment of the cell. It catalyzes the deamination of enamine/imine intermediates to yield 2-ketobutyrate and ammonia. It is required for the detoxification of reactive intermediates of IlvA due to their highly nucleophilic abilities. Involved in the isoleucine biosynthesis. May have a role in the purine metabolism.^[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

The yabJ gene in Bacillus subtilis is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The molecular mechanism of YabJ is unknown. YabJ is a member of a large, widely distributed family of proteins of unknown biochemical function. The 1.7-A crystal structure of YabJ reveals a trimeric organization with extensive buried hydrophobic surface and an internal water-filled cavity. The most important finding in the structure is a deep, narrow cleft between subunits lined with nine side chains that are invariant among the 25 most similar homologs. This conserved site is proposed to be a binding or catalytic site for a ligand or substrate that is common to YabJ and other members of the YER057c/YjgF/UK114 family of proteins.

Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family.,Sinha S, Rappu P, Lange SC, Mantsala P, Zalkin H, Smith JL Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13074-9. PMID:10557275^[2]

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

References

↑ Lambrecht JA, Flynn JM, Downs DM. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J Biol Chem. 2012 Jan 27;287(5):3454-61. doi: 10.1074/jbc.M111.304477. Epub 2011 , Nov 17. PMID:22094463 doi:http://dx.doi.org/10.1074/jbc.M111.304477
↑ Sinha S, Rappu P, Lange SC, Mantsala P, Zalkin H, Smith JL. Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family. Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13074-9. PMID:10557275

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/1qd9"

@@ Line 3: / Line 3: @@
 <StructureSection load='1qd9' size='340' side='right'caption='[[1qd9]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qd9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QD9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QD9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qd9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QD9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=EMC:ETHYL+MERCURY+ION'>EMC</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=EMC:ETHYL+MERCURY+ION'>EMC</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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=1qd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qd9 OCA], [http://pdbe.org/1qd9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qd9 RCSB], [http://www.ebi.ac.uk/pdbsum/1qd9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qd9 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=1qd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qd9 OCA], [https://pdbe.org/1qd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qd9 RCSB], [https://www.ebi.ac.uk/pdbsum/1qd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qd9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RIDA_BACSU RIDA_BACSU]] Accelerates the release of ammonia from reactive enamine/imine intermediates of the PLP-dependent threonine dehydratase (IlvA) in the low water environment of the cell. It catalyzes the deamination of enamine/imine intermediates to yield 2-ketobutyrate and ammonia. It is required for the detoxification of reactive intermediates of IlvA due to their highly nucleophilic abilities. Involved in the isoleucine biosynthesis. May have a role in the purine metabolism.<ref>PMID:22094463</ref>
+[[https://www.uniprot.org/uniprot/RIDA_BACSU RIDA_BACSU]] Accelerates the release of ammonia from reactive enamine/imine intermediates of the PLP-dependent threonine dehydratase (IlvA) in the low water environment of the cell. It catalyzes the deamination of enamine/imine intermediates to yield 2-ketobutyrate and ammonia. It is required for the detoxification of reactive intermediates of IlvA due to their highly nucleophilic abilities. Involved in the isoleucine biosynthesis. May have a role in the purine metabolism.<ref>PMID:22094463</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1qd9

From Proteopedia

Revision as of 09:54, 15 September 2021

Bacillus subtilis YABJ

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