5sy4

From Proteopedia

(Difference between revisions)

Current revision

Atomic resolution structure of reduced E. coli YajL

Structural highlights

5sy4 is a 2 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 0.98Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YAJL_ECOLI Protein deglycase that repairs methylglyoxal- and glyoxal-glycated amino acids and proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteines, arginines and lysines residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) (PubMed:25416785) (By similarity). Displays a covalent chaperone activity with sulfenylated thiol proteins by forming mixed disulfides with members of the thiol proteome, and preferentially with sulfenylated cellular proteins, upon oxidative stress; these mixed disulfides can be subsequently reduced by low-molecular-weight thiols to regenerate YajL and reduced proteins (PubMed:22157000, PubMed:22321799). Involved in biogenesis of ribosomal proteins, probably as a ribosomal protein-folding chaperone. Confers resistance to oxidative stress. The chaperone activity reported for YajL is probably recruited to execute its deglycase activity, to interact with non-native glycated proteins and gain access to partially buried glycated sites.[UniProtKB:Q99497]^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 A) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 A H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [dO-O = 2.542(2) A]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.,Lin J, Pozharski E, Wilson MA Biochemistry. 2016 Dec 30. doi: 10.1021/acs.biochem.6b00906. PMID:27989121^[6]

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

References

↑ Kthiri F, Le HT, Gautier V, Caldas T, Malki A, Landoulsi A, Bohn C, Bouloc P, Richarme G. Protein aggregation in a mutant deficient in yajL, the bacterial homolog of the Parkinsonism-associated protein DJ-1. J Biol Chem. 2010 Apr 2;285(14):10328-36. doi: 10.1074/jbc.M109.077529. Epub 2010, Feb 2. PMID:20124404 doi:http://dx.doi.org/10.1074/jbc.M109.077529
↑ Kthiri F, Gautier V, Le HT, Prere MF, Fayet O, Malki A, Landoulsi A, Richarme G. Translational defects in a mutant deficient in YajL, the bacterial homolog of the parkinsonism-associated protein DJ-1. J Bacteriol. 2010 Dec;192(23):6302-6. doi: 10.1128/JB.01077-10. Epub 2010 Oct 1. PMID:20889753 doi:http://dx.doi.org/10.1128/JB.01077-10
↑ Le HT, Gautier V, Kthiri F, Malki A, Messaoudi N, Mihoub M, Landoulsi A, An YJ, Cha SS, Richarme G. YajL, prokaryotic homolog of parkinsonism-associated protein DJ-1, functions as a covalent chaperone for thiol proteome. J Biol Chem. 2012 Feb 17;287(8):5861-70. doi: 10.1074/jbc.M111.299198. Epub 2011 , Dec 7. PMID:22157000 doi:http://dx.doi.org/10.1074/jbc.M111.299198
↑ Gautier V, Le HT, Malki A, Messaoudi N, Caldas T, Kthiri F, Landoulsi A, Richarme G. YajL, the prokaryotic homolog of the Parkinsonism-associated protein DJ-1, protects cells against protein sulfenylation. J Mol Biol. 2012 Aug 24;421(4-5):662-70. doi: 10.1016/j.jmb.2012.01.047. Epub, 2012 Feb 1. PMID:22321799 doi:http://dx.doi.org/10.1016/j.jmb.2012.01.047
↑ Richarme G, Mihoub M, Dairou J, Bui LC, Leger T, Lamouri A. Parkinsonism-associated protein DJ-1/Park7 is a major protein deglycase that repairs methylglyoxal- and glyoxal-glycated cysteine, arginine, and lysine residues. J Biol Chem. 2015 Jan 16;290(3):1885-97. doi: 10.1074/jbc.M114.597815. Epub 2014 , Nov 21. PMID:25416785 doi:http://dx.doi.org/10.1074/jbc.M114.597815
↑ Lin J, Pozharski E, Wilson MA. Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons. Biochemistry. 2016 Dec 30. doi: 10.1021/acs.biochem.6b00906. PMID:27989121 doi:http://dx.doi.org/10.1021/acs.biochem.6b00906

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5sy4"

Categories: Escherichia coli | Large Structures | Lin J | Wilson MA

@@ Line 3: / Line 3: @@
 <StructureSection load='5sy4' size='340' side='right'caption='[[5sy4]], [[Resolution|resolution]] 0.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5sy4]] is a 2 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=5SY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SY4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5sy4]] is a 2 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=5SY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SY4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 0.98&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">thiJ, ACU57_11870, AM266_04520, ERS085365_02411, ERS085416_01937, ERS139211_01908, ERS150873_01827, PU15_11320, PU38_04800, SK85_00449 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5sy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sy4 OCA], [http://pdbe.org/5sy4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sy4 RCSB], [http://www.ebi.ac.uk/pdbsum/5sy4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sy4 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=5sy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sy4 OCA], [https://pdbe.org/5sy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sy4 RCSB], [https://www.ebi.ac.uk/pdbsum/5sy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sy4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/YAJL_ECOLI YAJL_ECOLI] Protein deglycase that repairs methylglyoxal- and glyoxal-glycated amino acids and proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteines, arginines and lysines residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) (PubMed:25416785) (By similarity). Displays a covalent chaperone activity with sulfenylated thiol proteins by forming mixed disulfides with members of the thiol proteome, and preferentially with sulfenylated cellular proteins, upon oxidative stress; these mixed disulfides can be subsequently reduced by low-molecular-weight thiols to regenerate YajL and reduced proteins (PubMed:22157000, PubMed:22321799). Involved in biogenesis of ribosomal proteins, probably as a ribosomal protein-folding chaperone. Confers resistance to oxidative stress. The chaperone activity reported for YajL is probably recruited to execute its deglycase activity, to interact with non-native glycated proteins and gain access to partially buried glycated sites.[UniProtKB:Q99497]<ref>PMID:20124404</ref> <ref>PMID:20889753</ref> <ref>PMID:22157000</ref> <ref>PMID:22321799</ref> <ref>PMID:25416785</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Lin, J]]
+[[Category: Lin J]]
-[[Category: Wilson, M A]]
+[[Category: Wilson MA]]
-[[Category: Chaperone]]
-[[Category: Dj-1/pfpi superfamily nucleophile elbow]]

5sy4

From Proteopedia

Current revision

Atomic resolution structure of reduced E. coli YajL

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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