1vi2: Difference between revisions

Revision as of 16:35, 21 February 2008

Crystal structure of shikimate-5-dehydrogenase with NAD

OverviewOverview

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

About this StructureAbout this Structure

1VI2 is a Single protein structure of sequence from Escherichia coli with and as ligands. Active as Shikimate dehydrogenase, with EC number 1.1.1.25 Full crystallographic information is available from OCA.

ReferenceReference

Structural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins. 2005 Sep 1;60(4):787-96. PMID:16021622

Page seeded by OCA on Thu Feb 21 15:35:31 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1vi2.gif|left|200px]]<br /><applet load="1vi2" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1vi2.gif|left|200px]]<br /><applet load="1vi2" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1vi2, resolution 2.10&Aring;" />
 '''Crystal structure of shikimate-5-dehydrogenase with NAD'''<br />
 ==Overview==
-The targets of the Structural GenomiX (SGX) bacterial genomics project, were proteins conserved in multiple prokaryotic organisms with no obvious, sequence homolog in the Protein Data Bank of known structures. The outcome, of this work was 80 structures, covering 60 unique sequences and 49, different genes. Experimental phase determination from proteins, incorporating Se-Met was carried out for 45 structures with most of the, remainder solved by molecular replacement using members of the, experimentally phased set as search models. An automated tool was, developed to deposit these structures in the Protein Data Bank, along with, the associated X-ray diffraction data (including refined experimental, phases) and experimentally confirmed sequences. BLAST comparisons of the, SGX structures with structures that had appeared in the Protein Data Bank, over the intervening 3.5 years since the SGX target list had been compiled, identified homologs for 49 of the 60 unique sequences represented by the, SGX structures. This result indicates that, for bacterial structures that, are relatively easy to express, purify, and crystallize, the structural, coverage of gene space is proceeding rapidly. More distant, sequence-structure relationships between the SGX and PDB structures were, investigated using PDB-BLAST and Combinatorial Extension (CE). Only one, structure, SufD, has a truly unique topology compared to all folds in the, PDB.
+The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.
 ==About this Structure==
-VI2 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 SO4 and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VI2 OCA].
+VI2 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=SO4:'>SO4</scene> and <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Shikimate_dehydrogenase Shikimate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.25 1.1.1.25] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VI2 OCA].
 ==Reference==
@@ Line 19: / Line 19: @@
 [[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:52:10 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:35:31 2008''