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| | {{STRUCTURE_2g6v| PDB=2g6v | SCENE= }} | | {{STRUCTURE_2g6v| PDB=2g6v | SCENE= }} |
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| - | '''The crystal structure of ribD from Escherichia coli'''
| + | ===The crystal structure of ribD from Escherichia coli=== |
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| - | ==Overview==
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| - | We have determined the crystal structure of the bi-functional deaminase/reductase enzyme from Escherichia coli (EcRibD) that catalyzes two consecutive reactions during riboflavin biosynthesis. The polypeptide chain of EcRibD is folded into two domains where the 3D structure of the N-terminal domain (1-145) is similar to cytosine deaminase and the C-terminal domain (146-367) is similar to dihydrofolate reductase. We showed that EcRibD is dimeric and compared our structure to tetrameric RibG, an ortholog from Bacillus subtilis (BsRibG). We have also determined the structure of EcRibD in two binary complexes with the oxidized cofactor (NADP(+)) and with the substrate analogue ribose-5-phosphate (RP5) and superposed these two in order to mimic the ternary complex. Based on this superposition we propose that the invariant Asp200 initiates the reductive reaction by abstracting a proton from the bound substrate and that the pro-R proton from C4 of the cofactor is transferred to C1 of the substrate. A highly flexible loop is found in the reductase active site (159-173) that appears to control cofactor and substrate binding to the reductase active site and was therefore compared to the corresponding Met20 loop of E. coli dihydrofolate reductase (EcDHFR). Lys152, identified by comparing substrate analogue (RP5) coordination in the reductase active site of EcRibD with the homologous reductase from Methanocaldococcus jannaschii (MjaRED), is invariant among bacterial RibD enzymes and could contribute to the various pathways taken during riboflavin biosynthesis in bacteria and yeast.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_17765262}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 17765262 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_17765262}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Structural genomic]] | | [[Category: Structural genomic]] |
| | [[Category: Structural proteomics in europe]] | | [[Category: Structural proteomics in europe]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Apr 13 08:19:22 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 16:06:13 2008'' |
Revision as of 13:06, 29 July 2008
Template:STRUCTURE 2g6v
The crystal structure of ribD from Escherichia coli
Template:ABSTRACT PUBMED 17765262
About this Structure
2G6V is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism., Stenmark P, Moche M, Gurmu D, Nordlund P, J Mol Biol. 2007 Oct 12;373(1):48-64. Epub 2006 Dec 8. PMID:17765262
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