2cfm: Difference between revisions
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[[Image:2cfm.gif|left|200px]] | [[Image:2cfm.gif|left|200px]] | ||
'''ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS''' | {{Structure | ||
|PDB= 2cfm |SIZE=350|CAPTION= <scene name='initialview01'>2cfm</scene>, resolution 1.80Å | |||
|SITE= <scene name='pdbsite=AC1:Amp+Binding+Site+For+Chain+A'>AC1</scene> | |||
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=AMP:ADENOSINE MONOPHOSPHATE'>AMP</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/DNA_ligase_(ATP) DNA ligase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.1 6.5.1.1] | |||
|GENE= | |||
}} | |||
'''ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2CFM is a [ | 2CFM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CFM OCA]. | ||
==Reference== | ==Reference== | ||
The closed structure of an archaeal DNA ligase from Pyrococcus furiosus., Nishida H, Kiyonari S, Ishino Y, Morikawa K, J Mol Biol. 2006 Jul 28;360(5):956-67. Epub 2006 Jun 12. PMID:[http:// | The closed structure of an archaeal DNA ligase from Pyrococcus furiosus., Nishida H, Kiyonari S, Ishino Y, Morikawa K, J Mol Biol. 2006 Jul 28;360(5):956-67. Epub 2006 Jun 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16820169 16820169] | ||
[[Category: DNA ligase (ATP)]] | [[Category: DNA ligase (ATP)]] | ||
[[Category: Pyrococcus furiosus]] | [[Category: Pyrococcus furiosus]] | ||
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[[Category: protein-nucleotide complex]] | [[Category: protein-nucleotide complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:14:45 2008'' | ||
Revision as of 17:14, 20 March 2008
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| , resolution 1.80Å | |||||||
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| Sites: | |||||||
| Ligands: | and | ||||||
| Activity: | DNA ligase (ATP), with EC number 6.5.1.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS
OverviewOverview
DNA ligases join single-strand breaks in double-stranded DNA, and are essential to maintain genome integrity in DNA metabolism. Here, we report the 1.8 A resolution structure of Pyrococcus furiosus DNA ligase (PfuLig), which represents the first full-length atomic view of an ATP-dependent eukaryotic-type DNA ligase. The enzyme comprises the N-terminal DNA-binding domain, the middle adenylation domain, and the C-terminal OB-fold domain. The architecture of each domain resembles those of human DNA ligase I, but the domain arrangements differ strikingly between the two enzymes. The closed conformation of the two "catalytic core" domains at the carboxyl terminus in PfuLig creates a small compartment, which holds a non-covalently bound AMP molecule. This domain rearrangement results from the "domain-connecting" role of the helical extension conserved at the C termini in archaeal and eukaryotic DNA ligases. The DNA substrate in the human open-ligase is replaced by motif VI in the Pfu closed-ligase. Both the shapes and electrostatic distributions are similar between motif VI and the DNA substrate, suggesting that motif VI in the closed state mimics the incoming substrate DNA. Two basic residues (R531 and K534) in motif VI reside within the active site pocket and interact with the phosphate group of the bound AMP. The crystallographic and functional analyses of mutant enzymes revealed that these two residues within the RxDK sequence play essential and complementary roles in ATP processing. This sequence is also conserved exclusively among the covalent nucleotidyltransferases, even including mRNA-capping enzymes with similar helical extensions at the C termini.
About this StructureAbout this Structure
2CFM is a Single protein structure of sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA.
ReferenceReference
The closed structure of an archaeal DNA ligase from Pyrococcus furiosus., Nishida H, Kiyonari S, Ishino Y, Morikawa K, J Mol Biol. 2006 Jul 28;360(5):956-67. Epub 2006 Jun 12. PMID:16820169
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