1gvh

From Proteopedia

(Difference between revisions)

Revision as of 06:32, 3 January 2018

The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unespected geometry of the distal heme pocket

Structural highlights

1gvh is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Activity:	6,7-dihydropteridine reductase, with EC number 1.5.1.34
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[HMP_ECOLI] Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate, which protects the bacterium from various noxious nitrogen compounds. Therefore, plays a central role in the inducible response to nitrosative stress. In the presence of oxygen and NADH, HMP has NADH oxidase activity, which leads to the generation of superoxide and H(2)O(2), both in vitro and in vivo, and it has been suggested that HMP might act as an amplifier of superoxide stress. Under anaerobic conditions, HMP also exhibits nitric oxide reductase and FAD reductase activities. However, all these reactions are much lower than NOD activity. Various electron acceptors are also reduced by HMP in vitro, including dihydropterine, ferrisiderophores, ferric citrate, cytochrome c, nitrite, S-nitrosoglutathione, and alkylhydroperoxides. However, it is unknown if these reactions are of any biological significance in vivo.

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 x-ray structure of ferric unliganded lipid-free Escherichia coli flavohemoglobin has been solved to a resolution of 2.2 A and refined to an R-factor of 19%. The overall fold is similar to that of ferrous lipid-bound Alcaligenes eutrophus flavohemoglobin with the notable exception of the E helix positioning within the globin domain and a rotation of the NAD binding module with respect to the FAD-binding domain accompanied by a substantial rearrangement of the C-terminal region. An inspection of the heme environment in E. coli flavohemoglobin reveals an unexpected architecture of the distal pocket. In fact, the distal site is occupied by the isopropyl side chain Leu-E11 that shields the heme iron from the residues in the topological positions predicted to interact with heme iron-bound ligands, namely Tyr-B10 and Gln-E7, and stabilizes a pentacoordinate ferric iron species. Ligand binding properties are consistent with the presence of a pentacoordinate species in solution as indicated by a very fast second order combination rates with imidazole and azide. Surprisingly, imidazole, cyanide, and azide binding profiles at equilibrium are not accounted for by a single site titration curve but are biphasic and strongly suggest the presence of two distinct conformers within the liganded species.

The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket.,Ilari A, Bonamore A, Farina A, Johnson KA, Boffi A J Biol Chem. 2002 Jun 28;277(26):23725-32. Epub 2002 Apr 18. PMID:11964402^[1]

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

References

↑ Ilari A, Bonamore A, Farina A, Johnson KA, Boffi A. The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unexpected geometry of the distal heme pocket. J Biol Chem. 2002 Jun 28;277(26):23725-32. Epub 2002 Apr 18. PMID:11964402 doi:10.1074/jbc.M202228200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1gvh"

@@ Line 1: / Line 1: @@
-==THE X-RAY STRUCTURE OF FERRIC ESCHERICHIA COLI FLAVOHEMOGLOBIN REVEALS AN UNESPECTED GEOMETRY OF THE DISTAL HEME POCKET==
+==The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unespected geometry of the distal heme pocket==
 <StructureSection load='1gvh' size='340' side='right' caption='[[1gvh]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
 == Structural highlights ==
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dihydropteridine_reductase 6,7-dihydropteridine reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.34 1.5.1.34] </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=1gvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gvh OCA], [http://pdbe.org/1gvh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gvh RCSB], [http://www.ebi.ac.uk/pdbsum/1gvh PDBsum]</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=1gvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gvh OCA], [http://pdbe.org/1gvh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gvh RCSB], [http://www.ebi.ac.uk/pdbsum/1gvh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gvh ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gv/1gvh_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gv/1gvh_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1gvh

From Proteopedia

Revision as of 06:32, 3 January 2018

The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unespected geometry of the distal heme pocket

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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