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2vcl

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Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in the substrate free form

Structural highlights

2vcl is a 1 chain structure with sequence from Bpprm. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	2vck, 2vgr
Activity:	Phycoerythrobilin synthase, with EC number 1.3.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PEBS_BPPRM] Plays a role in phycoerythrobilin biosynthesis, the red pigment chromophore photosynthetically active biliproteins of the host cyanobacteria. Uses a four-electron reduction to carry out the reactions catalyzed by two enzymes (EC 1.3.7.2 and EC 1.3.7.3) in host.

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 reddish purple open chain tetrapyrrole pigment phycoerythrobilin (PEB; A(lambdamax) approximately 550 nm) is an essential chromophore of the light-harvesting phycobiliproteins of most cyanobacteria, red algae, and cryptomonads. The enzyme phycoerythrobilin synthase (PebS), recently discovered in a marine virus infecting oceanic cyanobacteria of the genus Prochlorococcus (cyanophage PSSM-2), is a new member of the ferredoxin-dependent bilin reductase (FDBR) family. In a formal four-electron reduction, the substrate biliverdin IXalpha is reduced to yield 3Z-PEB, a reaction that commonly requires the action of two individual FDBRs. The first reaction catalyzed by PebS is the reduction of the 15,16-methine bridge of the biliverdin IXalpha tetrapyrrole system. This reaction is exclusive to PEB biosynthetic enzymes. The second reduction site is the A-ring 2,3,3(1),3(2)-diene system, the most common target of FDBRs. Here, we present the first crystal structures of a PEB biosynthetic enzyme. Structures of the substrate complex were solved at 1.8- and 2.1-A resolution and of the substrate-free form at 1.55-A resolution. The overall folding revealed an alpha/beta/alpha-sandwich with similarity to the structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA). The substrate-binding site is located between the central beta-sheet and C-terminal alpha-helices. Eight refined molecules with bound substrate, from two different crystal forms, revealed a high flexibility of the substrate-binding pocket. The substrate was found to be either in a planar porphyrin-like conformation or in a helical conformation and is coordinated by a conserved aspartate/asparagine pair from the beta-sheet side. From the alpha-helix side, a conserved highly flexible aspartate/proline pair is involved in substrate binding and presumably catalysis.

Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form.,Dammeyer T, Hofmann E, Frankenberg-Dinkel N J Biol Chem. 2008 Oct 10;283(41):27547-54. Epub 2008 Jul 28. PMID:18662988^[1]

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

References

↑ Dammeyer T, Hofmann E, Frankenberg-Dinkel N. Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form. J Biol Chem. 2008 Oct 10;283(41):27547-54. Epub 2008 Jul 28. PMID:18662988 doi:10.1074/jbc.M803765200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vcl"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vcl' size='340' side='right'caption='[[2vcl]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vcl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpprm Bpprm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VCL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vcl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpprm Bpprm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VCL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vck|2vck]], [[2vgr|2vgr]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vck|2vck]], [[2vgr|2vgr]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phycoerythrobilin_synthase Phycoerythrobilin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.6 1.3.7.6] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phycoerythrobilin_synthase Phycoerythrobilin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.6 1.3.7.6] </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=2vcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vcl OCA], [http://pdbe.org/2vcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vcl RCSB], [http://www.ebi.ac.uk/pdbsum/2vcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vcl 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=2vcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vcl OCA], [https://pdbe.org/2vcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vcl RCSB], [https://www.ebi.ac.uk/pdbsum/2vcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vcl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PEBS_BPPRM PEBS_BPPRM]] Plays a role in phycoerythrobilin biosynthesis, the red pigment chromophore photosynthetically active biliproteins of the host cyanobacteria. Uses a four-electron reduction to carry out the reactions catalyzed by two enzymes (EC 1.3.7.2 and EC 1.3.7.3) in host.
+[[https://www.uniprot.org/uniprot/PEBS_BPPRM PEBS_BPPRM]] Plays a role in phycoerythrobilin biosynthesis, the red pigment chromophore photosynthetically active biliproteins of the host cyanobacteria. Uses a four-electron reduction to carry out the reactions catalyzed by two enzymes (EC 1.3.7.2 and EC 1.3.7.3) in host.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2vcl

From Proteopedia

Current revision

Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in the substrate free form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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