This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1o57
From Proteopedia
(New page: 200px<br /><applet load="1o57" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o57, resolution 2.20Å" /> '''CRYSTAL STRUCTURE OF...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1o57.gif|left|200px]]<br /><applet load="1o57" size=" | + | [[Image:1o57.gif|left|200px]]<br /><applet load="1o57" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1o57, resolution 2.20Å" /> | caption="1o57, resolution 2.20Å" /> | ||
'''CRYSTAL STRUCTURE OF THE PURINE OPERON REPRESSOR OF BACILLUS SUBTILIS'''<br /> | '''CRYSTAL STRUCTURE OF THE PURINE OPERON REPRESSOR OF BACILLUS SUBTILIS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The purine repressor from Bacillus subtilis, PurR, represses transcription | + | The purine repressor from Bacillus subtilis, PurR, represses transcription from a number of genes with functions in the synthesis, transport, and metabolism of purines. The 2.2-A crystal structure of PurR reveals a two-domain protein organized as a dimer. The larger C-terminal domain belongs to the PRT structural family, in accord with a sequence motif for binding the inducer phosphoribosylpyrophosphate (PRPP). The PRT domain is fused to a smaller N-terminal domain that belongs to the winged-helix family of DNA binding proteins. A positively charged surface on the winged-helix domain likely binds specific DNA sequences in the recognition site. A second positively charged surface surrounds the PRPP site at the opposite end of the PurR dimer. Conserved amino acids in the sequences of PurR homologs in 21 gram-positive bacteria cluster on the proposed recognition surface of the winged-helix domain and around the PRPP binding site at the opposite end of the molecule, supporting a common function of DNA and PRPP binding for all of the proteins. The structure supports a binding mechanism in which extended regions of DNA interact with extensive protein surface. Unlike most PRT proteins, which are phosphoribosyltransferases (PRTases), PurR lacks catalytic activity. This is explained by a tyrosine side chain that blocks the site for a nucleophile cosubstrate in PRTases. Thus, B. subtilis has adapted an enzyme fold to serve as an effector-binding domain and has used it in a novel combination with the DNA-binding winged-helix domain as a repressor of purine genes. |
==About this Structure== | ==About this Structure== | ||
| - | 1O57 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with SO4, EPE, P6G, 2PE, PG4 and 1PE as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 1O57 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=EPE:'>EPE</scene>, <scene name='pdbligand=P6G:'>P6G</scene>, <scene name='pdbligand=2PE:'>2PE</scene>, <scene name='pdbligand=PG4:'>PG4</scene> and <scene name='pdbligand=1PE:'>1PE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1P41. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O57 OCA]. |
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Krahn, J.]] | [[Category: Krahn, J.]] | ||
| - | [[Category: Shin, B | + | [[Category: Shin, B S.]] |
| - | [[Category: Sinha, S | + | [[Category: Sinha, S C.]] |
| - | [[Category: Smith, J | + | [[Category: Smith, J L.]] |
| - | [[Category: Tomchick, D | + | [[Category: Tomchick, D R.]] |
[[Category: Zalkin, H.]] | [[Category: Zalkin, H.]] | ||
[[Category: 1PE]] | [[Category: 1PE]] | ||
| Line 32: | Line 32: | ||
[[Category: transcription regulation]] | [[Category: transcription regulation]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:13:33 2008'' |
Revision as of 12:13, 21 February 2008
|
CRYSTAL STRUCTURE OF THE PURINE OPERON REPRESSOR OF BACILLUS SUBTILIS
Overview
The purine repressor from Bacillus subtilis, PurR, represses transcription from a number of genes with functions in the synthesis, transport, and metabolism of purines. The 2.2-A crystal structure of PurR reveals a two-domain protein organized as a dimer. The larger C-terminal domain belongs to the PRT structural family, in accord with a sequence motif for binding the inducer phosphoribosylpyrophosphate (PRPP). The PRT domain is fused to a smaller N-terminal domain that belongs to the winged-helix family of DNA binding proteins. A positively charged surface on the winged-helix domain likely binds specific DNA sequences in the recognition site. A second positively charged surface surrounds the PRPP site at the opposite end of the PurR dimer. Conserved amino acids in the sequences of PurR homologs in 21 gram-positive bacteria cluster on the proposed recognition surface of the winged-helix domain and around the PRPP binding site at the opposite end of the molecule, supporting a common function of DNA and PRPP binding for all of the proteins. The structure supports a binding mechanism in which extended regions of DNA interact with extensive protein surface. Unlike most PRT proteins, which are phosphoribosyltransferases (PRTases), PurR lacks catalytic activity. This is explained by a tyrosine side chain that blocks the site for a nucleophile cosubstrate in PRTases. Thus, B. subtilis has adapted an enzyme fold to serve as an effector-binding domain and has used it in a novel combination with the DNA-binding winged-helix domain as a repressor of purine genes.
About this Structure
1O57 is a Single protein structure of sequence from Bacillus subtilis with , , , , and as ligands. This structure supersedes the now removed PDB entry 1P41. Full crystallographic information is available from OCA.
Reference
The purine repressor of Bacillus subtilis: a novel combination of domains adapted for transcription regulation., Sinha SC, Krahn J, Shin BS, Tomchick DR, Zalkin H, Smith JL, J Bacteriol. 2003 Jul;185(14):4087-98. PMID:12837783
Page seeded by OCA on Thu Feb 21 14:13:33 2008
Categories: Bacillus subtilis | Single protein | Krahn, J. | Shin, B S. | Sinha, S C. | Smith, J L. | Tomchick, D R. | Zalkin, H. | 1PE | 2PE | EPE | P6G | PG4 | SO4 | Dna binding | Domain recombination | Helix-turn-helix domain | Phosphoribosyltranseferases | Purine operon repressor | Transcription regulation
