4d4z

From Proteopedia

(Difference between revisions)

Current revision

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:	, , ,
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:http://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:http://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:http://dx.doi.org/10.1016/j.str.2015.03.002

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://proteopedia.org/wiki/index.php/4d4z"

Categories: Homo sapiens | Large Structures | Han Z | Hilgenfeld R | Sakai N

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol==
-<StructureSection load='4d4z' size='340' side='right' caption='[[4d4z]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='4d4z' size='340' side='right'caption='[[4d4z]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4d4z]] is a 2 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D4Z FirstGlance]. <br>
+<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"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d50|4d50]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyhypusine_monooxygenase Deoxyhypusine monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.29 1.14.99.29] </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=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>
-<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=4d4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d4z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d4z RCSB], [http://www.ebi.ac.uk/pdbsum/4d4z PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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 ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4d4z" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Deoxyhypusine monooxygenase]]
+[[Category: Homo sapiens]]
-[[Category: Han, Z]]
+[[Category: Large Structures]]
-[[Category: Hilgenfeld, R]]
+[[Category: Han Z]]
-[[Category: Sakai, N]]
+[[Category: Hilgenfeld R]]
-[[Category: Eif-5a]]
+[[Category: Sakai N]]
-[[Category: Hypusine]]
-[[Category: Oxidoreductase]]

4d4z

From Proteopedia

Current revision

STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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