4d4z: Difference between revisions

Latest revision as of 11:17, 9 May 2024

STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol

Structural highlights

4d4z is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	B3P, FE, GOL, OH
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DOHH_HUMAN Catalyzes the hydroxylation of the N(6)-(4-aminobutyl)-L-lysine intermediate to form hypusine, an essential post-translational modification only found in mature eIF-5A factor.[HAMAP-Rule:MF_03101]^[1] ^[2]

Publication Abstract from PubMed

Deoxyhypusine hydroxylase (DOHH) is a non-heme diiron enzyme involved in the posttranslational modification of a critical lysine residue of eukaryotic translation initiation factor 5A (eIF-5A) to yield the unusual amino acid residue hypusine. This modification is essential for the role of eIF-5A in translation and in nuclear export of a group of specific mRNAs. The diiron center of human DOHH (hDOHH) forms a peroxo-diiron(III) intermediate (hDOHHperoxo) when its reduced form reacts with O2. hDOHHperoxo has a lifetime exceeding that of the peroxo intermediates of other diiron enzymes by several orders of magnitude. Here we report the 1.7-A crystal structures of hDOHHperoxo and a complex with glycerol. The structure of hDOHHperoxo reveals the presence of a mu-1,2-peroxo-diiron(III) species at the active site. Augmented by UV/Vis and Mossbauer spectroscopic studies, the crystal structures offer explanations for the extreme longevity of hDOHHperoxo and illustrate how the enzyme specifically recognizes its only substrate, deoxyhypusine-eIF-5A.

Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination.,Han Z, Sakai N, Bottger LH, Klinke S, Hauber J, Trautwein AX, Hilgenfeld R Structure. 2015 Apr 9. pii: S0969-2126(15)00080-5. doi:, 10.1016/j.str.2015.03.002. PMID:25865244^[3]

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

References

↑ Park JH, Aravind L, Wolff EC, Kaevel J, Kim YS, Park MH. Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme. Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):51-6. Epub 2005 Dec 21. PMID:16371467 doi:https://dx.doi.org/0509348102
↑ Vu VV, Emerson JP, Martinho M, Kim YS, Munck E, Park MH, Que L Jr. Human deoxyhypusine hydroxylase, an enzyme involved in regulating cell growth, activates O2 with a nonheme diiron center. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14814-9. doi:, 10.1073/pnas.0904553106. Epub 2009 Aug 19. PMID:19706422 doi:https://dx.doi.org/10.1073/pnas.0904553106
↑ Han Z, Sakai N, Bottger LH, Klinke S, Hauber J, Trautwein AX, Hilgenfeld R. Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination. Structure. 2015 Apr 9. pii: S0969-2126(15)00080-5. doi:, 10.1016/j.str.2015.03.002. PMID:25865244 doi:https://dx.doi.org/10.1016/j.str.2015.03.002

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Park JH, Aravind L, Wolff EC, Kaevel J, Kim YS, Park MH. Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme. Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):51-6. Epub 2005 Dec 21. PMID:16371467 doi:https://dx.doi.org/0509348102

[2] Vu VV, Emerson JP, Martinho M, Kim YS, Munck E, Park MH, Que L Jr. Human deoxyhypusine hydroxylase, an enzyme involved in regulating cell growth, activates O2 with a nonheme diiron center. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14814-9. doi:, 10.1073/pnas.0904553106. Epub 2009 Aug 19. PMID:19706422 doi:https://dx.doi.org/10.1073/pnas.0904553106

[3] Han Z, Sakai N, Bottger LH, Klinke S, Hauber J, Trautwein AX, Hilgenfeld R. Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination. Structure. 2015 Apr 9. pii: S0969-2126(15)00080-5. doi:, 10.1016/j.str.2015.03.002. PMID:25865244 doi:https://dx.doi.org/10.1016/j.str.2015.03.002

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[2]

[3]

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4d4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D4Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></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=4d4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4z OCA], [https://pdbe.org/4d4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d4z RCSB], [https://www.ebi.ac.uk/pdbsum/4d4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d4z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DOHH_HUMAN DOHH_HUMAN]] Catalyzes the hydroxylation of the N(6)-(4-aminobutyl)-L-lysine intermediate to form hypusine, an essential post-translational modification only found in mature eIF-5A factor.[HAMAP-Rule:MF_03101]<ref>PMID:16371467</ref> <ref>PMID:19706422</ref>
+[https://www.uniprot.org/uniprot/DOHH_HUMAN DOHH_HUMAN] Catalyzes the hydroxylation of the N(6)-(4-aminobutyl)-L-lysine intermediate to form hypusine, an essential post-translational modification only found in mature eIF-5A factor.[HAMAP-Rule:MF_03101]<ref>PMID:16371467</ref> <ref>PMID:19706422</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4d4z: Difference between revisions

Latest revision as of 11:17, 9 May 2024

STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol

Structural highlights

Function

Publication Abstract from PubMed

References

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