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.

1uc9

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8

Structural highlights

1uc9 is a 2 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.38Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

LYSX_THET8 Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.^[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 thermophilic bacterium Thermus thermophilus synthesizes lysine through the alpha-aminoadipate pathway, which uses alpha-aminoadipate as a biosynthetic intermediate of lysine. LysX is the essential enzyme in this pathway, and is believed to catalyze the acylation of alpha-aminoadipate. We have determined the crystal structures of LysX and its complex with ADP at 2.0A and 2.38A resolutions, respectively. LysX is composed of three alpha+beta domains, each composed of a four to five-stranded beta-sheet core flanked by alpha-helices. The C-terminal and central domains form an ATP-grasp fold, which is responsible for ATP binding. LysX has two flexible loop regions, which are expected to play an important role in substrate binding and protection. In spite of the low level of sequence identity, the overall fold of LysX is surprisingly similar to that of other ATP-grasp fold proteins, such as D-Ala:D-Ala ligase, PurT-encoded glycinamide ribonucleotide transformylase, glutathione synthetase, and synapsin I. In particular, they share a similar spatial arrangement of the amino acid residues around the ATP-binding site. This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity.

Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8.,Sakai H, Vassylyeva MN, Matsuura T, Sekine S, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S J Mol Biol. 2003 Sep 19;332(3):729-40. PMID:12963379^[2]

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

References

↑ Horie A, Tomita T, Saiki A, Kono H, Taka H, Mineki R, Fujimura T, Nishiyama C, Kuzuyama T, Nishiyama M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat Chem Biol. 2009 Sep;5(9):673-9. doi: 10.1038/nchembio.198. Epub 2009 Jul 20. PMID:19620981 doi:http://dx.doi.org/10.1038/nchembio.198
↑ Sakai H, Vassylyeva MN, Matsuura T, Sekine S, Gotoh K, Nishiyama M, Terada T, Shirouzu M, Kuramitsu S, Vassylyev DG, Yokoyama S. Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8. J Mol Biol. 2003 Sep 19;332(3):729-40. PMID:12963379

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/1uc9"

@@ Line 3: / Line 3: @@
 <StructureSection load='1uc9' size='340' side='right'caption='[[1uc9]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1uc9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UC9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 2.38&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1uc8|1uc8]]</div></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=1uc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uc9 OCA], [https://pdbe.org/1uc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uc9 RCSB], [https://www.ebi.ac.uk/pdbsum/1uc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uc9 ProSAT], [https://www.topsan.org/Proteins/RSGI/1uc9 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8]] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>
+[https://www.uniprot.org/uniprot/LYSX_THET8 LYSX_THET8] Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.<ref>PMID:19620981</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
 [[Category: Large Structures]]
-[[Category: Kuramitsu, S]]
+[[Category: Thermus thermophilus]]
-[[Category: Matsuura, T]]
+[[Category: Kuramitsu S]]
-[[Category: Nishiyama, M]]
+[[Category: Matsuura T]]
-[[Category: Structural genomic]]
+[[Category: Nishiyama M]]
-[[Category: Sakai, H]]
+[[Category: Sakai H]]
-[[Category: Sekine, S]]
+[[Category: Sekine S]]
-[[Category: Shirouzu, M]]
+[[Category: Shirouzu M]]
-[[Category: Terada, T]]
+[[Category: Terada T]]
-[[Category: Vassylyev, D G]]
+[[Category: Vassylyev DG]]
-[[Category: Vassylyeva, M N]]
+[[Category: Vassylyeva MN]]
-[[Category: Yokoyama, S]]
+[[Category: Yokoyama S]]
-[[Category: Alpha-aminoadipate pathway]]
-[[Category: Biosynthetic protein]]
-[[Category: Lysine biosynthesis]]
-[[Category: Rsgi]]

1uc9

From Proteopedia

Current revision

Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8

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