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5UJ0
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BU of 5uj0 by Molmil
Structure of T4Pnkp 3' phosphatase covalently bound to BeF3
Descriptor: GLYCEROL, MAGNESIUM ION, Polynucleotide kinase
Authors:Shuman, S, Chatterjee, D.
Deposit date:2017-01-16
Release date:2017-02-08
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Truncated T4Pnk covalently bound to BeF3
To Be Published
3KGD
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BU of 3kgd by Molmil
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
6C36
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BU of 6c36 by Molmil
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
6C33
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BU of 6c33 by Molmil
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
6C35
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BU of 6c35 by Molmil
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
5U32
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BU of 5u32 by Molmil
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:2024-03-06
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
6EDE
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BU of 6ede by Molmil
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
6E3A
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BU of 6e3a by Molmil
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:2023-10-11
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
6C34
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BU of 6c34 by Molmil
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
2OWO
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BU of 2owo by Molmil
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
2QY2
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BU of 2qy2 by Molmil
Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domainm.
Descriptor: ACETATE ION, CITRATE ANION, Probable mRNA-capping enzyme
Authors:Shuman, S, Benarroch, D, Smith, P.
Deposit date:2007-08-13
Release date:2008-04-01
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:Characterization of a trifunctional mimivirus mRNA capping enzyme and crystal structure of the RNA triphosphatase domain.
Structure, 16, 2008
6NHX
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BU of 6nhx by Molmil
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
6NHZ
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BU of 6nhz by Molmil
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
3N9B
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BU of 3n9b by Molmil
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
3N9D
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BU of 3n9d by Molmil
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
6VDD
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BU of 6vdd by Molmil
POL domain of Pol1 from M. smegmatis complex with DNA primer-template and dNTP
Descriptor: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*TP*A*(DCT))-3'), DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ...
Authors:Shuman, S, Goldgur, Y, Ghosh, S.
Deposit date:2019-12-24
Release date:2020-02-12
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (1.9 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
6VDC
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BU of 6vdc by Molmil
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
6VDE
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BU of 6vde by Molmil
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
6U05
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BU of 6u05 by Molmil
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
6TZX
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BU of 6tzx by Molmil
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
6U03
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BU of 6u03 by Molmil
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
6U00
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BU of 6u00 by Molmil
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
6TZO
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BU of 6tzo by Molmil
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
6TZM
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BU of 6tzm by Molmil
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
4MDE
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BU of 4mde by Molmil
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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PDB entries from 2024-03-27

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