1dag: Difference between revisions

Revision as of 22:44, 30 June 2008

This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.

File:1dag.png

Template:STRUCTURE 1dag

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID AND 5'-ADENOSYL-METHYLENE-TRIPHOSPHATEDETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID AND 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE

Template:ABSTRACT PUBMED 7669756

About this StructureAbout this Structure

1DAG is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate., Huang W, Jia J, Gibson KJ, Taylor WS, Rendina AR, Schneider G, Lindqvist Y, Biochemistry. 1995 Sep 5;34(35):10985-95. PMID:7669756

Page seeded by OCA on Mon Jun 30 22:44:32 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1dag.gif|left|200px]]
+{{Seed}}
+[[Image:1dag.png|left|200px]]
 <!--
@@ Line 9: / Line 10: @@
 {{STRUCTURE_1dag|  PDB=1dag  |  SCENE=  }}
-'''DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID AND 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE'''
+===DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID AND 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE===
-==Overview==
+<!--
-The crystal structures of six complexes of homodimeric Escherichia coli dethiobiotin synthetase with a variety of substrates, substrate analogs, and products have been determined to high resolution. These include (1) the binary complex of dethiobiotin synthetase and the N7-carbamate of 7,8-diaminononanoic acid, (2) the binary complex of enzyme and the alternate substrate, 3-(1-aminoethyl)-nonanedioic acid, (3) the binary complex of enzyme with the product ADP, (4) the quaternary complex of enzyme, ADP, the N7-carbamate of 7,8-diaminononanoic acid, and Ca2+, (5) the ternary complex of enzyme, the ATP analog adenylyl (beta, gamma-methylene)diphosphonate, and the N7-carbamate of 7,8-diaminononanoic acid, and (6) the quaternary complex of enzyme, the ATP analog adenylyl (beta, gamma-methylene)diphosphonate, 7,8-diaminononanoic acid, and Mn2+. One molecule of each substrate binds to one monomer of the enzyme. ADP and the ATP analogue bind to the classical mononucleotide binding fold with the phosphate groups close to the phosphate binding loop Gly8--Thr16 between beta-strand beta 1 and the N-terminus of alpha-helix alpha 1. The adenine ring is bound in a pocket between beta-strands beta 6 and beta 7. In the quaternary complex with Mn2+, the metal binding site is found in the vicinity of the beta- and gamma-phosphate groups. Two oxygen atoms from the phosphates and oxygen atoms from the side chains of Asp54, Thr16, and Glu115 are ligands to the Mn2+ ion in the quaternary complex. In the complex with ADP and the N7-carbamate of 7,8-diaminononanoic acid prepared in the presence of Ca2+ ions, a different metal binding site is found. The Ca2+ ion is coordinated to an oxygen atom of the alpha-phosphate group of the nucleotide, the side chain of Asp54, and solvent molecules. The 7,8-diaminononanoic acid substrate molecule interacts with residues from both subunits, making the dimer the minimal functional unit. The diamino group binds between the loops after beta 2 and beta 4, and the terminal carboxyl group at the hydrophobic tail of the substrate interacts with the amino terminus of helix alpha 5 and with the side chain of Tyr187 in helix alpha 6 of the second subunit at the monomer-monomer interface. Strong additional electron density close to the N7 nitrogen atom of the 7,8-diaminononanoic acid substrate in some complexes indicates that, even in the absence of added bicarbonate in the crystallization mixture, the carbamylated intermediate is formed in the crystal.(ABSTRACT TRUNCATED AT 400 WORDS)
+The line below this paragraph, {{ABSTRACT_PUBMED_7669756}}, adds the Publication Abstract to the page
+(as it appears on PubMed at http://www.pubmed.gov), where 7669756 is the PubMed ID number.
+-->
+{{ABSTRACT_PUBMED_7669756}}
 ==About this Structure==
@@ Line 31: / Line 35: @@
 [[Category: Ligase]]
 [[Category: Magnesium]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:37:41 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:44:32 2008''