2vbv

From Proteopedia

(Difference between revisions)

Revision as of 11:26, 17 June 2020

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN

Structural highlights

2vbv is a 2 chain structure with sequence from Atcc 43067. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Related:	2p3m, 2vbs, 2vbt, 2vbu
Activity:	CTP-dependent riboflavin kinase, with EC number 2.7.1.161
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RIFK_METJA] Catalyzes the CTP-dependent phosphorylation of riboflavin (vitamin B2) to form flavin mononucleotide (FMN). Can also utilize UTP as the phosphate donor, although less efficiently, and it is unclear if ATP and GTP can also serve as substrates (PubMed:18245297) or not (PubMed:18073108).^[1] ^[2]

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

Proteins of the cradle-loop barrel metafold are formed by duplication of a conserved betaalphabeta-element, suggesting a common evolutionary origin from an ancestral group of nucleic acid-binding proteins. The basal fold within this metafold, the RIFT barrel, is also found in a wide range of enzymes, whose homologous relationship with the nucleic acid-binding group is unclear. We have characterized a protein family that is intermediate in sequence and structure between the basal group of cradle-loop barrels and one family of RIFT-barrel enzymes, the riboflavin kinases. We report the structure, substrate-binding mode, and catalytic activity for one of these proteins, Methanocaldococcus jannaschii Mj0056, which is an archaeal riboflavin kinase. Mj0056 is unusual in utilizing CTP rather than ATP as the donor nucleotide, and sequence conservation in the relevant residues suggests that this is a general feature of archaeal riboflavin kinases.

A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.,Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M Structure. 2007 Dec;15(12):1577-90. PMID:18073108^[3]

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

References

↑ Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M. A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure. 2007 Dec;15(12):1577-90. PMID:18073108 doi:10.1016/j.str.2007.09.027
↑ Mashhadi Z, Zhang H, Xu H, White RH. Identification and characterization of an archaeon-specific riboflavin kinase. J Bacteriol. 2008 Apr;190(7):2615-8. doi: 10.1128/JB.01900-07. Epub 2008 Feb 1. PMID:18245297 doi:http://dx.doi.org/10.1128/JB.01900-07
↑ Ammelburg M, Hartmann MD, Djuranovic S, Alva V, Koretke KK, Martin J, Sauer G, Truffault V, Zeth K, Lupas AN, Coles M. A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure. 2007 Dec;15(12):1577-90. PMID:18073108 doi:10.1016/j.str.2007.09.027

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/2vbv"

@@ Line 1: / Line 1: @@
 ==Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN==
-<StructureSection load='2vbv' size='340' side='right' caption='[[2vbv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='2vbv' size='340' side='right'caption='[[2vbv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VBV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VBV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VBV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VBV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2p3m|2p3m]], [[2vbs|2vbs]], [[2vbt|2vbt]], [[2vbu|2vbu]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/CTP-dependent_riboflavin_kinase CTP-dependent riboflavin kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.161 2.7.1.161] </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=2vbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vbv OCA], [http://pdbe.org/2vbv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vbv RCSB], [http://www.ebi.ac.uk/pdbsum/2vbv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vbv ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vbv OCA], [http://pdbe.org/2vbv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vbv RCSB], [http://www.ebi.ac.uk/pdbsum/2vbv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vbv ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 36: / Line 36: @@
 [[Category: Atcc 43067]]
 [[Category: CTP-dependent riboflavin kinase]]
+[[Category: Large Structures]]
 [[Category: Ammelburg, M]]
 [[Category: Djuranovic, S]]

2vbv

From Proteopedia

Revision as of 11:26, 17 June 2020

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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