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2GKE
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Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP
Descriptor: (2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID, ACETIC ACID, Diaminopimelate epimerase, ...
Authors:Pillai, B, Cherney, M.M, Diaper, C.M, Sutherland, A, Blanchard, J.S, Vederas, J.C, James, M.N.
Deposit date:2006-04-01
Release date:2006-05-16
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target.
Proc.Natl.Acad.Sci.Usa, 103, 2006
2GKJ
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BU of 2gkj by Molmil
Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor DL-AZIDAP
Descriptor: (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID, ACETIC ACID, Diaminopimelate epimerase
Authors:Pillai, B, Cherney, M.M, Diaper, C.M, Sutherland, A, Blanchard, J.S, Vederas, J.C, James, M.N.
Deposit date:2006-04-02
Release date:2006-05-16
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target.
Proc.Natl.Acad.Sci.Usa, 103, 2006
1GQZ
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BU of 1gqz by Molmil
Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A
Descriptor: DIAMINOPIMELATE EPIMERASE
Authors:Roper, D.I, Huyton, T, Turkenburg, J.P.
Deposit date:2001-12-07
Release date:2003-06-12
Last modified:2023-12-13
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis.
Acta Crystallogr. D Biol. Crystallogr., 60, 2004
6D1V
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BU of 6d1v by Molmil
Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA
Descriptor: CHLORIDE ION, Diaminopimelate epimerase, GLYCEROL, ...
Authors:Gao, A, Serganov, A.
Deposit date:2018-04-12
Release date:2018-05-23
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
Nucleic Acids Res., 46, 2018
5HA4
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Structure of a diaminopimelate epimerase from Acinetobacter baumannii
Descriptor: (4R)-2-METHYLPENTANE-2,4-DIOL, CHLORIDE ION, Diaminopimelate epimerase
Authors:Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Deposit date:2015-12-30
Release date:2016-01-27
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Structure of a diaminopimelate epimerase from Acinetobacter baumannii
to be published
3EJX
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Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana in complex with LL-AziDAP
Descriptor: (2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID, Diaminopimelate epimerase, chloroplastic
Authors:Pillai, B, Moorthie, V.A, Cherney, M.M, Vederas, J.C, James, M.N.G.
Deposit date:2008-09-18
Release date:2009-02-17
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis.
J.Mol.Biol., 385, 2009
5H2Y
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Crystal structure of reduced DapF from Corynebacterium glutamicum
Descriptor: Diaminopimelate epimerase
Authors:Sagong, H.-Y, Kim, K.-J.
Deposit date:2016-10-18
Release date:2016-11-09
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Sci Rep, 7, 2017
5H2G
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Crystal structure of oxidized DapF from Corynebacterium glutamicum
Descriptor: Diaminopimelate epimerase, GLYCEROL, SULFATE ION
Authors:Sagong, H.-Y, Kim, K.-J.
Deposit date:2016-10-15
Release date:2016-11-09
Last modified:2020-09-09
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Sci Rep, 7, 2017
4IJZ
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Crystal structure of diaminopimelate epimerase from Escherichia coli
Descriptor: Diaminopimelate epimerase, NITRATE ION
Authors:Hor, L, Dobson, R.C.J, Hutton, C.A, Perugini, M.A.
Deposit date:2012-12-24
Release date:2013-02-20
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2 Å)
Cite:Dimerization of bacterial diaminopimelate epimerase is essential for catalysis
J.Biol.Chem., 288, 2013
4IK0
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Crystal structure of diaminopimelate epimerase Y268A mutant from Escherichia coli
Descriptor: Diaminopimelate epimerase, IODIDE ION
Authors:Hor, L, Dobson, R.C.J, Hutton, C.A, Perugini, M.A.
Deposit date:2012-12-24
Release date:2013-02-20
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Dimerization of bacterial diaminopimelate epimerase is essential for catalysis
J.Biol.Chem., 288, 2013
6VCL
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BU of 6vcl by Molmil
Crystal structure of E.coli RppH-DapF in complex with pppGpp, Mg2+ and F-
Descriptor: CHLORIDE ION, Diaminopimelate epimerase, FLUORIDE ION, ...
Authors:Gao, A, Vasilyev, N, Kaushik, A, Duan, W, Serganov, A.
Deposit date:2019-12-21
Release date:2020-02-05
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.06 Å)
Cite:Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Nucleic Acids Res., 48, 2020
7VDY
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BU of 7vdy by Molmil
Crystal structure of O-ureidoserine racemase
Descriptor: O-ureido-serine racemase, SULFATE ION
Authors:Oda, K, Matoba, Y.
Deposit date:2021-09-07
Release date:2021-12-15
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Crystal structure of O-ureidoserine racemase found in the d-cycloserine biosynthetic pathway.
Proteins, 90, 2022
6D1Q
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BU of 6d1q by Molmil
Crystal structure of E. coli RppH-DapF complex, monomer
Descriptor: CHLORIDE ION, Diaminopimelate epimerase, GLYCEROL, ...
Authors:Gao, A, Serganov, A.
Deposit date:2018-04-12
Release date:2018-05-23
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
Nucleic Acids Res., 46, 2018
2Q9J
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BU of 2q9j by Molmil
Crystal structure of the C217S mutant of diaminopimelate epimerase
Descriptor: 1,2-ETHANEDIOL, Diaminopimelate epimerase, SULFATE ION
Authors:Pillai, B, Cherney, M, Diaper, C.M, Sutherland, A, Blanchard, J.S, Vederas, J.C.
Deposit date:2007-06-12
Release date:2007-10-23
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.
Biochem.Biophys.Res.Commun., 363, 2007
5YGU
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BU of 5ygu by Molmil
Crystal structure of Escherichia coli (strain K12) mRNA Decapping Complex RppH-DapF
Descriptor: Diaminopimelate epimerase, IODIDE ION, L(+)-TARTARIC ACID, ...
Authors:Wang, Q, Guan, Z.Y, Zhang, D.L, Zou, T.T, Yin, P.
Deposit date:2017-09-27
Release date:2018-06-06
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.298 Å)
Cite:DapF stabilizes the substrate-favoring conformation of RppH to stimulate its RNA-pyrophosphohydrolase activity in Escherichia coli.
Nucleic Acids Res., 46, 2018
2Q9H
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BU of 2q9h by Molmil
Crystal structure of the C73S mutant of diaminopimelate epimerase
Descriptor: ACETIC ACID, Diaminopimelate epimerase, L(+)-TARTARIC ACID
Authors:Pillai, B, Cherney, M, Diaper, C.M, Sutherland, A, Blanchard, J.S, Vederas, J.C, James, M.N.G.
Deposit date:2007-06-12
Release date:2007-10-23
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.
Biochem.Biophys.Res.Commun., 363, 2007
3EKM
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BU of 3ekm by Molmil
Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP
Descriptor: (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID, Diaminopimelate epimerase, chloroplastic
Authors:Pillai, B, Moorthie, V.A, Cherney, M.M, van Belkum, M.J, Vederas, J.C, James, M.N.G.
Deposit date:2008-09-19
Release date:2009-02-17
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis.
J.Mol.Biol., 385, 2009
6VCM
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BU of 6vcm by Molmil
Crystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F-
Descriptor: CHLORIDE ION, Diaminopimelate epimerase, FLUORIDE ION, ...
Authors:Gao, A, Vasilyev, N, Kaushik, A, Duan, W, Serganov, A.
Deposit date:2019-12-21
Release date:2020-02-05
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Nucleic Acids Res., 48, 2020
2OTN
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BU of 2otn by Molmil
Crystal structure of the catalytically active form of diaminopimelate epimerase from Bacillus anthracis
Descriptor: Diaminopimelate epimerase
Authors:Matho, M.H, Fukuda, K, Santelli, E, Jaroszewski, L, Liddington, R.C, Roper, D.
Deposit date:2007-02-08
Release date:2008-03-04
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal structure and inhibition of a catalytically active form of diaminopimelate epimerase (DapF)from Bacillus anthracis
To be Published
5M47
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BU of 5m47 by Molmil
Crystal structure of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate
Descriptor: 2,6-DIAMINOPIMELIC ACID, Diaminopimelate epimerase
Authors:Sagong, H.-Y, Kim, K.-J.
Deposit date:2016-10-18
Release date:2016-11-02
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (2.59 Å)
Cite:Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Sci Rep, 7, 2017
3FVE
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BU of 3fve by Molmil
Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF
Descriptor: 2,3-DIHYDROXY-1,4-DITHIOBUTANE, Diaminopimelate epimerase, GLYCEROL
Authors:Usha, V, Dover, L.G, Roper, D.I, Futterer, K, Besra, G.S.
Deposit date:2009-01-15
Release date:2009-01-27
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis
Acta Crystallogr.,Sect.D, 65, 2009
6VCK
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BU of 6vck by Molmil
Crystal structure of E.coli RppH-DapF in complex with GDP, Mg2+ and F-
Descriptor: CHLORIDE ION, Diaminopimelate epimerase, FLUORIDE ION, ...
Authors:Gao, A, Vasilyev, N, Kaushik, A, Duan, W, Serganov, A.
Deposit date:2019-12-21
Release date:2020-02-05
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.69 Å)
Cite:Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Nucleic Acids Res., 48, 2020
1BWZ
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BU of 1bwz by Molmil
DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE
Descriptor: PROTEIN (DIAMINOPIMELATE EPIMERASE)
Authors:Cirilli, M, Zheng, R, Scapin, G, Blanchard, J.S.
Deposit date:1998-09-29
Release date:1998-12-16
Last modified:2017-10-04
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.
Biochemistry, 37, 1998
6D13
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Crystal structure of E.coli RppH-DapF complex
Descriptor: CHLORIDE ION, Diaminopimelate epimerase, IODIDE ION, ...
Authors:Gao, A, Serganov, A.
Deposit date:2018-04-11
Release date:2018-05-23
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (3.06 Å)
Cite:Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
Nucleic Acids Res., 46, 2018

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PDB entries from 2024-03-27

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