4kp2

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of homoaconitase large subunit from methanococcus jannaschii (MJ1003)

Structural highlights

4kp2 is a 2 chain structure with sequence from Methanocaldococcus jannaschii DSM 2661. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.504Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HACA_METJA Hydro-lyase with broad substrate specificity for cis-unsaturated tricarboxylic acids. Catalyzes both the reversible dehydration of (R)-homocitrate ((R)-2-hydroxybutane-1,2,4-tricarboxylate) to produce cis-homoaconitate ((Z)-but-1-ene-1,2,4-tricarboxylate), and its hydration to homoisocitrate ((1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate). Is also able to hydrate the analogous longer chain substrates cis-homo(2)-aconitate, cis-homo(3)-aconitate, and even the non-physiological cis-homo(4)-aconitate with similar efficiency. These reactions are part of the biosynthesis pathway of coenzyme B. Can also catalyze the hydration of maleate to (R)-malate, and that of cis-aconitate. Can not catalyze the hydration of citraconate and the dehydration of (S)-homocitrate, citramalate, 2-isopropylmalate, 3-isopropylmalate, citrate or threo-DL-isocitrate.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and isopropylmalate (IPM) isomerases. They have a common Fe-S cluster-binding site and catalyze the isomerization of specific substrates by sequential dehydration and hydration. The archaeon Methanococcus jannaschii contains two aconitase family proteins, IPM isomerase and homoaconitase, which have 50% sequence identity. These two enzymes are heterodimeric proteins composed of large and small subunits encoded by separate genes. Although structures have been reported for the small subunits of the two enzymes, the first structures of oxidized and reduced forms of the large subunit of IPM isomerase (ox-MJ0499 and red-MJ0499, respectively) from M. jannaschii are reported here at 1.8 and 2.7 A resolution, respectively, together with the structure of the large subunit of homoaconitase (MJ1003) at 2.5 A resolution. The structures of both proteins have unbound Fe-S clusters and contain a fourth cysteine in the active site. The active site of MJ1003 is homologous to that of aconitase, whereas MJ0499 has significant structural distortion at the active site compared with aconitase. In addition, significant large conformational changes were observed in the active site of red-MJ0499 when compared with ox-MJ0499. The active sites of the two proteins adopt two different states before changing to the Fe-S cluster-bound `activated' state observed in aconitase. MJ1003 has an `open' active site, which forms an active pocket for the cluster, while ox-MJ0499 has a `closed' active site, with four cysteines in disulfide bonds. These data will be helpful in understanding the biochemical mechanism of clustering of the Fe-S protein family.

Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii.,Lee EH, Lee K, Hwang KY Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):922-31. doi:, 10.1107/S1399004713033762. Epub 2014 Mar 19. PMID:24699638^[4]

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

References

↑ Drevland RM, Waheed A, Graham DE. Enzymology and evolution of the pyruvate pathway to 2-oxobutyrate in Methanocaldococcus jannaschii. J Bacteriol. 2007 Jun;189(12):4391-400. Epub 2007 Apr 20. PMID:17449626 doi:http://dx.doi.org/10.1128/JB.00166-07
↑ Drevland RM, Jia Y, Palmer DR, Graham DE. Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J Biol Chem. 2008 Oct 24;283(43):28888-96. Epub 2008 Sep 2. PMID:18765671 doi:http://dx.doi.org/M802159200
↑ Jeyakanthan J, Drevland RM, Gayathri DR, Velmurugan D, Shinkai A, Kuramitsu S, Yokoyama S, Graham DE. Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit. Biochemistry. 2010 Mar 30;49(12):2687-96. PMID:20170198 doi:10.1021/bi901766z
↑ Lee EH, Lee K, Hwang KY. Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii. Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):922-31. doi:, 10.1107/S1399004713033762. Epub 2014 Mar 19. PMID:24699638 doi:http://dx.doi.org/10.1107/S1399004713033762

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4kp2"

Categories: Large Structures | Methanocaldococcus jannaschii DSM 2661 | Hwang KY | Lee EH

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4kp2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KP2 FirstGlance]. <br>
-</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=4kp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kp2 OCA], [https://pdbe.org/4kp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kp2 RCSB], [https://www.ebi.ac.uk/pdbsum/4kp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kp2 ProSAT]</span></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]] 2.504&#8491;</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=4kp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kp2 OCA], [https://pdbe.org/4kp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kp2 RCSB], [https://www.ebi.ac.uk/pdbsum/4kp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kp2 ProSAT]</span></td></tr>
 </table>
 == Function ==

4kp2

From Proteopedia

Current revision

Crystal structure of homoaconitase large subunit from methanococcus jannaschii (MJ1003)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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