Motion in Taq DNA polymerase I [taqpol]

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Classification Known Fragment Motion, Hinge Mechanism [F-h-2]

Structures
2KTQ open ternary complex
3KTQ closed ternary complex
4KTQ binary polI/DNA complex

Description
The large fragment of DNA polymerase I resembles a hand, with the DNA bound in the region formed by the "thumb", "palm", and "fingers". In the crystal structures from Thermus aquaticus, the fingers domain rotates downwards towards the bound DNA to add a nucleotide to the growing strand.

Particular values describing motion
Overall RMS deviation = 2.09
Experimental Methods = x (Traditional x-ray)

References
Y Li, S Korolev, and G Waksman (1998). Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymeras I: structural basis for nucleotide incorporation. EMBO Journal, 17:7514-7525.

Data and Graphics
Movie of taqpol Morph of 2KTQ->3KTQ

GO terms associated with structures
Molecular functionDNA binding, 5'-3' exonuclease activity, DNA-directed DNA polymerase activity, nuclease activity
Cellular componentintracellular
Biological processDNA replication

Morphs

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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Taq polymerase 2KTQ [ A ] 3KTQ [ A ] 540


Automatic morphs
Morph Morph name Structure #1 Structure #2 Residues
va1qssA-4ktqA DNA Polymerase I 1qss [ A ] 4ktq [ A ] 539
va1qtmA-4ktqA DNA Polymerase I 1qtm [ A ] 4ktq [ A ] 539
va1qsyA-4ktqA DNA Polymerase I 1qsy [ A ] 4ktq [ A ] 539

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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu