6U03
 
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | GUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, tRNA ligase | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2019-08-13 | | Release date: | 2019-11-06 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.849 Å) | | Cite: | Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Nucleic Acids Res., 47, 2019
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2QY2
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6U00
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | PHOSPHATE ION, tRNA ligase | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2019-08-13 | | Release date: | 2019-11-06 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.981 Å) | | Cite: | Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Nucleic Acids Res., 47, 2019
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6TZM
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, tRNA ligase | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2019-08-12 | | Release date: | 2019-11-06 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.714 Å) | | Cite: | Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Nucleic Acids Res., 47, 2019
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6U05
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, PHOSPHATE ION, ... | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2019-08-13 | | Release date: | 2019-11-06 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.948 Å) | | Cite: | Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Nucleic Acids Res., 47, 2019
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6TZX
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | INOSINE-5'-DIPHOSPHATE, PHOSPHATE ION, tRNA ligase | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2019-08-13 | | Release date: | 2019-11-06 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.529 Å) | | Cite: | Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Nucleic Acids Res., 47, 2019
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6TZO
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE, PHOSPHATE ION, tRNA ligase | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2019-08-12 | | Release date: | 2019-11-06 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.69 Å) | | Cite: | Atomic structures of the RNA end-healing 5'-OH kinase and 2',3'-cyclic phosphodiesterase domains of fungal tRNA ligase: conformational switches in the kinase upon binding of the GTP phosphate donor.
Nucleic Acids Res., 47, 2019
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3N9B
 | | Crystal Structure of the P. aeruginosa LigD phosphoesterase domain | | Descriptor: | CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MANGANESE (II) ION, ... | | Authors: | Shuman, S, Nair, P, Smith, P. | | Deposit date: | 2010-05-28 | | Release date: | 2010-08-11 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily
Proc.Natl.Acad.Sci.USA, 107, 2010
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3N9D
 | | Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain | | Descriptor: | MANGANESE (II) ION, Probable ATP-dependent DNA ligase, SULFATE ION, ... | | Authors: | Shuman, S, Nair, P, Smith, P. | | Deposit date: | 2010-05-28 | | Release date: | 2010-08-11 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily
Proc.Natl.Acad.Sci.USA, 107, 2010
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2OWO
 | | Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate | | Descriptor: | 26-MER, 5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3', 5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3', ... | | Authors: | Shuman, S, Nandakumar, J, Nair, P.A. | | Deposit date: | 2007-02-16 | | Release date: | 2007-05-15 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate.
Mol.Cell, 26, 2007
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5UJ0
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6NHZ
 | | mycobacterial DNA ligase D complexed with ATP and Mg | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, ATP-dependent DNA ligase, MAGNESIUM ION | | Authors: | Shuman, S, Unciuleac, M, Goldgur, Y. | | Deposit date: | 2018-12-24 | | Release date: | 2019-02-13 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.
J. Biol. Chem., 294, 2019
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6NHX
 | | mycobacterial DNA ligase D complexed with ATP and MES | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ADENOSINE-5'-TRIPHOSPHATE, ATP-dependent DNA ligase | | Authors: | Shuman, S, Unciuleac, M, Goldgur, Y. | | Deposit date: | 2018-12-24 | | Release date: | 2019-02-13 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.
J. Biol. Chem., 294, 2019
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3KGD
 | | Crystal structure of E. coli RNA 3' cyclase | | Descriptor: | ADENOSINE MONOPHOSPHATE, GLYCEROL, RNA 3'-terminal phosphate cyclase, ... | | Authors: | Shuman, S, Tanaka, N, Smith, P. | | Deposit date: | 2009-10-28 | | Release date: | 2010-04-21 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.68 Å) | | Cite: | Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.
Structure, 18, 2010
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5U32
 | | Crystal Structure of Fungal RNA Kinase | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, tRNA ligase | | Authors: | Shuman, S, Goldgur, Y, Remus, B.S. | | Deposit date: | 2016-12-01 | | Release date: | 2017-11-15 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.191 Å) | | Cite: | Structural basis for the GTP specificity of the RNA kinase domain of fungal tRNA ligase.
Nucleic Acids Res., 45, 2017
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6C34
 | | Mycobacterium smegmatis DNA flap endonuclease mutant D125N | | Descriptor: | 5'-3' exonuclease, MANGANESE (II) ION | | Authors: | Shuman, S, Goldgur, Y, Carl, A, Uson, M.L. | | Deposit date: | 2018-01-09 | | Release date: | 2018-03-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.
Nucleic Acids Res., 46, 2018
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6C35
 | | Mycobacterium smegmatis flap endonuclease mutant D148N | | Descriptor: | 5'-3' exonuclease, MANGANESE (II) ION | | Authors: | Shuman, S, Goldgur, Y, Carl, A, Uson, M.L. | | Deposit date: | 2018-01-09 | | Release date: | 2018-03-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.803 Å) | | Cite: | Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.
Nucleic Acids Res., 46, 2018
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6C33
 | | Mycobacterium smegmatis DNA flap endonuclease | | Descriptor: | 5'-3' exonuclease, MANGANESE (II) ION | | Authors: | Shuman, S, Goldgur, Y, Carl, A, Uson, M.L. | | Deposit date: | 2018-01-09 | | Release date: | 2018-03-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.
Nucleic Acids Res., 46, 2018
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6C36
 | | Mycobacterium smegmatis flap endonuclease mutant D208N | | Descriptor: | 5'-3' exonuclease, MANGANESE (II) ION, PHOSPHATE ION | | Authors: | Shuman, S, Goldgur, Y, Carl, A, Uson, M.L. | | Deposit date: | 2018-01-09 | | Release date: | 2018-03-28 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.
Nucleic Acids Res., 46, 2018
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4MDE
 | | Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA | | Descriptor: | DNA (5'-D(P*CP*CP*TP*GP*T)-3'), GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Shuman, S, Das, U, Wang, L.K, Smith, P, Jacewicz, A. | | Deposit date: | 2013-08-22 | | Release date: | 2013-11-06 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.
Nucleic Acids Res., 42, 2014
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4MDF
 | | Structure of bacterial polynucleotide kinase Michaelis complex bound to GTP and DNA | | Descriptor: | CITRIC ACID, DNA (5'-D(*CP*CP*TP*GP*T)-3'), GUANOSINE-5'-TRIPHOSPHATE, ... | | Authors: | Shuman, S, Das, U, Wang, L.K, Smith, P, Jacewicz, A. | | Deposit date: | 2013-08-22 | | Release date: | 2013-11-06 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.727 Å) | | Cite: | Structures of bacterial polynucleotide kinase in a Michaelis complex with GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.
Nucleic Acids Res., 42, 2014
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6EDE
 | | tRNA 2'-phosphotransferase | | Descriptor: | Probable RNA 2'-phosphotransferase, [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2018-08-09 | | Release date: | 2019-03-20 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.553 Å) | | Cite: | Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation.
Nat Commun, 10, 2019
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6E3A
 | | tRNA 2'-phosphotransferase | | Descriptor: | COENZYME A, Probable RNA 2'-phosphotransferase, [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate | | Authors: | Shuman, S, Goldgur, Y, Banerjee, A. | | Deposit date: | 2018-07-13 | | Release date: | 2019-03-20 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation.
Nat Commun, 10, 2019
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6VDC
 | | POL domain of Pol1 from M. smegmatis | | Descriptor: | DNA polymerase I, MANGANESE (II) ION | | Authors: | Shuman, S, Goldgur, Y, Ghosh, S. | | Deposit date: | 2019-12-24 | | Release date: | 2020-02-12 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.402 Å) | | Cite: | Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Nucleic Acids Res., 48, 2020
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6VDE
 | | Full-length M. smegmatis Pol1 | | Descriptor: | DNA polymerase I, MANGANESE (II) ION | | Authors: | Shuman, S, Goldgur, Y, Ghosh, S. | | Deposit date: | 2019-12-24 | | Release date: | 2020-02-12 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.713 Å) | | Cite: | Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.
Nucleic Acids Res., 48, 2020
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