1arz
From Proteopedia
(New page: 200px<br /><applet load="1arz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1arz, resolution 2.6Å" /> '''ESCHERICHIA COLI DIHY...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1arz.gif|left|200px]]<br /><applet load="1arz" size=" | + | [[Image:1arz.gif|left|200px]]<br /><applet load="1arz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1arz, resolution 2.6Å" /> | caption="1arz, resolution 2.6Å" /> | ||
'''ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE'''<br /> | '''ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Dihydrodipicolinate reductase catalyzes the NAD(P)H-dependent reduction of | + | Dihydrodipicolinate reductase catalyzes the NAD(P)H-dependent reduction of the alpha,beta-unsaturated cyclic imine dihydrodipicolinate to form the cyclic imine tetrahydrodipicolinate. The enzyme is a component of the biosynthetic pathway that leads to diaminopimelate and lysine in bacteria and higher plants. Because these pathways are unique to microorganisms and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds. The three-dimensional structure of the ternary complex of Escherichia coli dihydrodipicolinate reductase with NADH and the inhibitor 2,6-pyridinedicarboxylate has been solved using a combination of molecular replacement and noncrystallographic symmetry averaging procedures and refined against 2.6 A resolution data to a crystallographic R-factor of 21.4% (Rfree is 29.7%). The native enzyme is a 120 000 molecular weight tetramer of identical subunits. The refined crystallographic model contains a tetramer, three molecules of NADH, three molecules of inhibitor, one phosphate ion, and 186 water molecules per asymmetric unit. Each subunit consists of two domains connected by two flexible hinge regions. While three of the four subunits of the tetramer have a closed conformation, in which the nicotinamide ring of the cofactor bound to the N-terminal domain and the reducible carbon of the substrate bound to the substrate binding domain are about 3.5 A away, the fourth subunit is unliganded and shows an open conformation, suggesting that the enzyme undergoes a major conformational change upon binding of both substrates. The residues involved in binding of the inhibitor and the residues involved in catalysis have been identified on the basis of the three-dimensional structure. Site-directed mutants have been used to further characterize the role of these residues in binding and catalysis. A chemical mechanism for the enzyme, based on these and previously reported data, is proposed. |
==About this Structure== | ==About this Structure== | ||
| - | 1ARZ 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 PO4, K, NAD and PDC as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Dihydrodipicolinate_reductase Dihydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.26 1.3.1.26] Full crystallographic information is available from [http:// | + | 1ARZ 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=PO4:'>PO4</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=NAD:'>NAD</scene> and <scene name='pdbligand=PDC:'>PDC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Dihydrodipicolinate_reductase Dihydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.26 1.3.1.26] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARZ OCA]. |
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Blanchard, J | + | [[Category: Blanchard, J S.]] |
| - | [[Category: Reddy, S | + | [[Category: Reddy, S G.]] |
[[Category: Scapin, G.]] | [[Category: Scapin, G.]] | ||
[[Category: Zheng, R.]] | [[Category: Zheng, R.]] | ||
| Line 27: | Line 27: | ||
[[Category: reductase]] | [[Category: reductase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:47:41 2008'' |
Revision as of 09:47, 21 February 2008
|
ESCHERICHIA COLI DIHYDRODIPICOLINATE REDUCTASE IN COMPLEX WITH NADH AND 2,6 PYRIDINE DICARBOXYLATE
Overview
Dihydrodipicolinate reductase catalyzes the NAD(P)H-dependent reduction of the alpha,beta-unsaturated cyclic imine dihydrodipicolinate to form the cyclic imine tetrahydrodipicolinate. The enzyme is a component of the biosynthetic pathway that leads to diaminopimelate and lysine in bacteria and higher plants. Because these pathways are unique to microorganisms and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds. The three-dimensional structure of the ternary complex of Escherichia coli dihydrodipicolinate reductase with NADH and the inhibitor 2,6-pyridinedicarboxylate has been solved using a combination of molecular replacement and noncrystallographic symmetry averaging procedures and refined against 2.6 A resolution data to a crystallographic R-factor of 21.4% (Rfree is 29.7%). The native enzyme is a 120 000 molecular weight tetramer of identical subunits. The refined crystallographic model contains a tetramer, three molecules of NADH, three molecules of inhibitor, one phosphate ion, and 186 water molecules per asymmetric unit. Each subunit consists of two domains connected by two flexible hinge regions. While three of the four subunits of the tetramer have a closed conformation, in which the nicotinamide ring of the cofactor bound to the N-terminal domain and the reducible carbon of the substrate bound to the substrate binding domain are about 3.5 A away, the fourth subunit is unliganded and shows an open conformation, suggesting that the enzyme undergoes a major conformational change upon binding of both substrates. The residues involved in binding of the inhibitor and the residues involved in catalysis have been identified on the basis of the three-dimensional structure. Site-directed mutants have been used to further characterize the role of these residues in binding and catalysis. A chemical mechanism for the enzyme, based on these and previously reported data, is proposed.
About this Structure
1ARZ is a Single protein structure of sequence from Escherichia coli with , , and as ligands. Active as Dihydrodipicolinate reductase, with EC number 1.3.1.26 Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate., Scapin G, Reddy SG, Zheng R, Blanchard JS, Biochemistry. 1997 Dec 9;36(49):15081-8. PMID:9398235
Page seeded by OCA on Thu Feb 21 11:47:41 2008
