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5yvz

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Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and Fe(III)

Structural highlights

5yvz is a 1 chain structure with sequence from Methylacidiphilum infernorum V4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B3DUR4_METI4

Publication Abstract from PubMed

During lipopolysaccharide biosynthesis in several pathogens, including Burkholderia and Yersinia, 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) 3-hydroxylase, otherwise referred to as KdoO, converts Kdo to d-glycero-d-talo-oct-2-ulosonic acid (Ko) in an Fe(II)/alpha-ketoglutarate (alpha-KG)/O2-dependent manner. This conversion renders the bacterial outer membrane more stable and resistant to stresses such as an acidic environment. KdoO is a membrane-associated, deoxy-sugar hydroxylase that does not show significant sequence identity with any known enzymes, and its structural information has not been previously reported. Here, we report the biochemical and structural characterization of KdoO, Minf_1012 (KdoMI), from Methylacidiphilum infernorum V4. The de novo structure of KdoMI apoprotein indicates that KdoOMI consists of 13 alpha helices and 11 beta strands, and has the jelly roll fold containing a metal binding motif, HXDX111H. Structures of KdoMI bound to Co(II), KdoMI bound to alpha-KG and Fe(III), and KdoMI bound to succinate and Fe(III), in addition to mutagenesis analysis, indicate that His146, His260, and Asp148 play critical roles in Fe(II) binding, while Arg127, Arg162, Arg174, and Trp176 stabilize alpha-KG. It was also observed that His225 is adjacent to the active site and plays an important role in the catalysis of KdoOMI without affecting substrate binding, possibly being involved in oxygen activation. The crystal structure of KdoOMI is the first completed structure of a deoxy-sugar hydroxylase, and the data presented here have provided mechanistic insights into deoxy-sugar hydroxylase, KdoO, and lipopolysaccharide biosynthesis.

Biochemical and Structural Insights into an Fe(II)/alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO).,Joo SH, Pemble CW 4th, Yang EG, Raetz CRH, Chung HS J Mol Biol. 2018 Aug 7. pii: S0022-2836(18)30719-8. doi:, 10.1016/j.jmb.2018.07.029. PMID:30092253^[1]

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

References

↑ Joo SH, Pemble CW 4th, Yang EG, Raetz CRH, Chung HS. Biochemical and Structural Insights into an Fe(II)/alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO). J Mol Biol. 2018 Aug 7. pii: S0022-2836(18)30719-8. doi:, 10.1016/j.jmb.2018.07.029. PMID:30092253 doi:http://dx.doi.org/10.1016/j.jmb.2018.07.029

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/5yvz"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and Fe(III)==
-<StructureSection load='5yvz' size='340' side='right' caption='[[5yvz]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='5yvz' size='340' side='right'caption='[[5yvz]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yvz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yvz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylacidiphilum_infernorum_V4 Methylacidiphilum infernorum V4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YVZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5y7s|5y7s]], [[5yka|5yka]], [[5y9x|5y9x]], [[5y9y|5y9y]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5yvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvz OCA], [http://pdbe.org/5yvz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvz RCSB], [http://www.ebi.ac.uk/pdbsum/5yvz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvz 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=5yvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvz OCA], [https://pdbe.org/5yvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yvz RCSB], [https://www.ebi.ac.uk/pdbsum/5yvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvz ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B3DUR4_METI4 B3DUR4_METI4]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Chung, H S]]
+[[Category: Large Structures]]
-[[Category: Joo, S H]]
+[[Category: Methylacidiphilum infernorum V4]]
-[[Category: Pemble, C W]]
+[[Category: Chung HS]]
-[[Category: Raetz, C R]]
+[[Category: Joo SH]]
-[[Category: Biosynthetic protein]]
+[[Category: Pemble CW]]
-[[Category: Deoxysugar dioxygenase]]
+[[Category: Raetz CR]]
-[[Category: Kdo2-lipid a dioxygenase]]
-[[Category: Lps biosynthesis]]

5yvz

From Proteopedia

Current revision

Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and Fe(III)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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