2cjb: Difference between revisions

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Revision as of 17:16, 20 March 2008

File:2cjb.gif

, resolution 2.70Å

Sites:

Ligands:

, and

Activity:

Serine--tRNA ligase, with EC number 6.1.1.11

Coordinates:

save as pdb, mmCIF, xml

CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH SERINE

OverviewOverview

Methanogenic archaea possess unusual seryl-tRNA synthetase (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. The two types of SerRSs show only minimal sequence similarity, primarily within class II conserved motifs 1, 2 and 3. Here, we report a 2.5 A resolution crystal structure of the atypical methanogenic Methanosarcina barkeri SerRS and its complexes with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5'-O-(N-serylsulfamoyl)adenosine. The structures reveal two idiosyncratic features of methanogenic SerRSs: a novel N-terminal tRNA-binding domain and an active site zinc ion. The tetra-coordinated Zn2+ ion is bound to three conserved protein ligands (Cys306, Glu355 and Cys461) and binds the amino group of the serine substrate. The absolute requirement of the metal ion for enzymatic activity was confirmed by mutational analysis of the direct zinc ion ligands. This zinc-dependent serine recognition mechanism differs fundamentally from the one employed by the bacterial-type SerRSs. Consequently, SerRS represents the only known aminoacyl-tRNA synthetase system that evolved two distinct mechanisms for the recognition of the same amino-acid substrate.

About this StructureAbout this Structure

2CJB is a Single protein structure of sequence from Methanosarcina barkeri. Full crystallographic information is available from OCA.

ReferenceReference

Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition., Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N, EMBO J. 2006 Jun 7;25(11):2498-509. Epub 2006 May 4. PMID:16675947

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OCA

@@ Line 1: / Line 1: @@
-[[Image:2cjb.gif|left|200px]]<br /><applet load="2cjb" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2cjb.gif|left|200px]]
-caption="2cjb, resolution 2.70&Aring;" />
-'''CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH SERINE'''<br />
+ {{Structure
+|PDB= 2cjb |SIZE=350|CAPTION= <scene name='initialview01'>2cjb</scene>, resolution 2.70&Aring;
+|SITE= <scene name='pdbsite=AC1:SER+Binding+Site+For+Chain+A'>AC1</scene>
+|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=SER:SERINE'>SER</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11]
+|GENE=
+}}
+'''CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH SERINE'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-CJB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_barkeri Methanosarcina barkeri] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=SER:'>SER</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Serine--tRNA_ligase Serine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.11 6.1.1.11] Known structural/functional Site: <scene name='pdbsite=AC1:SER+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CJB OCA].
+CJB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_barkeri Methanosarcina barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CJB OCA].
 ==Reference==
-Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition., Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N, EMBO J. 2006 Jun 7;25(11):2498-509. Epub 2006 May 4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16675947 16675947]
+Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition., Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Soll D, Weygand-Durasevic I, Ban N, EMBO J. 2006 Jun 7;25(11):2498-509. Epub 2006 May 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16675947 16675947]
 [[Category: Methanosarcina barkeri]]
 [[Category: Serine--tRNA ligase]]
@@ Line 29: / Line 38: @@
 [[Category: zinc ion]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:49:14 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:16:06 2008''