2gpe: Difference between revisions

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[[Image:2gpe.gif|left|200px]]<br /><applet load="2gpe" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:2gpe.gif|left|200px]]<br /><applet load="2gpe" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2gpe, resolution 1.900Å" />

'''Structure of the DNA-binding domain of E. Coli Proline Utilization A (PUTA)'''<br />

==Overview==

PutA (proline utilization A) from Escherichia coli is a 1320-amino-acid, residue protein that is both a bifunctional proline catabolic enzyme and, an autogenous transcriptional repressor. Here, we report the first crystal, structure of a PutA DNA-binding domain along with functional analysis of a, mutant PutA defective in DNA binding. Crystals were grown using a, polypeptide corresponding to residues 1-52 of E. coli PutA (PutA52). The, 2.1 Angstrom resolution structure of PutA52 mutant Lys9Met was determined, using Se-Met MAD phasing, and the structure of native PutA52 was solved at, 1.9 Angstrom resolution using molecular replacement. Residues 3-46 form a, ribbon-helix-helix (RHH) substructure, thus establishing PutA as the, largest protein to contain an RHH domain. The PutA RHH domain forms the, intertwined dimer with tightly packed hydrophobic core that is, characteristic of the RHH family. The structures were used to examine the, three-dimensional context of residues conserved in PutA RHH domains., Homology modeling suggests that Lys9 and Thr5 contact DNA bases through, the major groove, while Arg15, Thr28, and His30 may interact with the, phosphate backbone. Lys9 is shown to be essential for specific recognition, of put control DNA using gel shift analysis of the Lys9Met mutant of, full-length PutA. Lys9 is disordered in the PutA52 structure, which, implies an induced-fit binding mechanism in which the side chain of Lys9, becomes ordered through interaction with DNA. These results provide new, insights into the structural basis of DNA recognition by PutA and reveal, three-dimensional structural details of the PutA dimer interface.

PutA (proline utilization A) from Escherichia coli is a 1320-amino-acid residue protein that is both a bifunctional proline catabolic enzyme and an autogenous transcriptional repressor. Here, we report the first crystal structure of a PutA DNA-binding domain along with functional analysis of a mutant PutA defective in DNA binding. Crystals were grown using a polypeptide corresponding to residues 1-52 of E. coli PutA (PutA52). The 2.1 Angstrom resolution structure of PutA52 mutant Lys9Met was determined using Se-Met MAD phasing, and the structure of native PutA52 was solved at 1.9 Angstrom resolution using molecular replacement. Residues 3-46 form a ribbon-helix-helix (RHH) substructure, thus establishing PutA as the largest protein to contain an RHH domain. The PutA RHH domain forms the intertwined dimer with tightly packed hydrophobic core that is characteristic of the RHH family. The structures were used to examine the three-dimensional context of residues conserved in PutA RHH domains. Homology modeling suggests that Lys9 and Thr5 contact DNA bases through the major groove, while Arg15, Thr28, and His30 may interact with the phosphate backbone. Lys9 is shown to be essential for specific recognition of put control DNA using gel shift analysis of the Lys9Met mutant of full-length PutA. Lys9 is disordered in the PutA52 structure, which implies an induced-fit binding mechanism in which the side chain of Lys9 becomes ordered through interaction with DNA. These results provide new insights into the structural basis of DNA recognition by PutA and reveal three-dimensional structural details of the PutA dimer interface.

==About this Structure==

2GPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with IMD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2GPE OCA].

2GPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=IMD:'>IMD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GPE OCA].

==Reference==

Line 13:

[[Category: Escherichia coli]]

[[Category: Single protein]]

[[Category: Jenkins, J.L.]]

[[Category: Jenkins, J L.]]

[[Category: Larson, J.]]

[[Category: Tanner, J.J.]]

[[Category: Tanner, J J.]]

[[Category: IMD]]

[[Category: dna-binding domain]]

Line 23:

[[Category: ribbon-helix-helix]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:33:59 2008''

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@@ Line 1: / Line 1: @@
-[[Image:2gpe.gif|left|200px]]<br /><applet load="2gpe" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2gpe.gif|left|200px]]<br /><applet load="2gpe" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2gpe, resolution 1.900&Aring;" />
 '''Structure of the DNA-binding domain of E. Coli Proline Utilization A (PUTA)'''<br />
 ==Overview==
-PutA (proline utilization A) from Escherichia coli is a 1320-amino-acid, residue protein that is both a bifunctional proline catabolic enzyme and, an autogenous transcriptional repressor. Here, we report the first crystal, structure of a PutA DNA-binding domain along with functional analysis of a, mutant PutA defective in DNA binding. Crystals were grown using a, polypeptide corresponding to residues 1-52 of E. coli PutA (PutA52). The, 2.1 Angstrom resolution structure of PutA52 mutant Lys9Met was determined, using Se-Met MAD phasing, and the structure of native PutA52 was solved at, 1.9 Angstrom resolution using molecular replacement. Residues 3-46 form a, ribbon-helix-helix (RHH) substructure, thus establishing PutA as the, largest protein to contain an RHH domain. The PutA RHH domain forms the, intertwined dimer with tightly packed hydrophobic core that is, characteristic of the RHH family. The structures were used to examine the, three-dimensional context of residues conserved in PutA RHH domains., Homology modeling suggests that Lys9 and Thr5 contact DNA bases through, the major groove, while Arg15, Thr28, and His30 may interact with the, phosphate backbone. Lys9 is shown to be essential for specific recognition, of put control DNA using gel shift analysis of the Lys9Met mutant of, full-length PutA. Lys9 is disordered in the PutA52 structure, which, implies an induced-fit binding mechanism in which the side chain of Lys9, becomes ordered through interaction with DNA. These results provide new, insights into the structural basis of DNA recognition by PutA and reveal, three-dimensional structural details of the PutA dimer interface.
+PutA (proline utilization A) from Escherichia coli is a 1320-amino-acid residue protein that is both a bifunctional proline catabolic enzyme and an autogenous transcriptional repressor. Here, we report the first crystal structure of a PutA DNA-binding domain along with functional analysis of a mutant PutA defective in DNA binding. Crystals were grown using a polypeptide corresponding to residues 1-52 of E. coli PutA (PutA52). The 2.1 Angstrom resolution structure of PutA52 mutant Lys9Met was determined using Se-Met MAD phasing, and the structure of native PutA52 was solved at 1.9 Angstrom resolution using molecular replacement. Residues 3-46 form a ribbon-helix-helix (RHH) substructure, thus establishing PutA as the largest protein to contain an RHH domain. The PutA RHH domain forms the intertwined dimer with tightly packed hydrophobic core that is characteristic of the RHH family. The structures were used to examine the three-dimensional context of residues conserved in PutA RHH domains. Homology modeling suggests that Lys9 and Thr5 contact DNA bases through the major groove, while Arg15, Thr28, and His30 may interact with the phosphate backbone. Lys9 is shown to be essential for specific recognition of put control DNA using gel shift analysis of the Lys9Met mutant of full-length PutA. Lys9 is disordered in the PutA52 structure, which implies an induced-fit binding mechanism in which the side chain of Lys9 becomes ordered through interaction with DNA. These results provide new insights into the structural basis of DNA recognition by PutA and reveal three-dimensional structural details of the PutA dimer interface.
 ==About this Structure==
-GPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with IMD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GPE OCA].
+GPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=IMD:'>IMD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GPE OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
-[[Category: Jenkins, J.L.]]
+[[Category: Jenkins, J L.]]
 [[Category: Larson, J.]]
-[[Category: Tanner, J.J.]]
+[[Category: Tanner, J J.]]
 [[Category: IMD]]
 [[Category: dna-binding domain]]
@@ Line 23: / Line 23: @@
 [[Category: ribbon-helix-helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:19:18 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:33:59 2008''