PDBsum entry 3pmn

Lyase,transferase/DNA

PDB id

3pmn

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Contents

			Protein chain

					312 a.a. *

			DNA/RNA

			Ligands

					1GC

			Metals

					_NA ×2


					_MG


					_MN ×3


					_CL ×2

			Waters ×202

* Residue conservation analysis

PDB id:

3pmn

Links

Name:

Lyase,transferase/DNA

Title:

Ternary crystal structure of polymerase lambda variant with a gt mispair at the primer terminus with mn2+ in the active site

Structure:

DNA polymerase lambda. Chain: a. Fragment: unp residues 242-575. Synonym: pol lambda, DNA polymerase beta-2, pol beta2, DNA polymerase kappa. Engineered: yes. 5'-d( Cp Gp Gp Cp Cp Tp Tp Ap Cp Tp G)-3'. Chain: b. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: poll. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

2.20Å

R-factor:

0.213

R-free:

0.243

Authors:

K.Bebenek,L.C.Pedersen,T.A.Kunkel

Key ref:

K.Bebenek et al. (2011). Replication infidelity via a mismatch with Watson-Crick geometry. Proc Natl Acad Sci U S A, 108, 1862-1867. PubMed id: 21233421

Date:

17-Nov-10

Release date:

02-Feb-11

PROCHECK

	Headers

	References

Protein chain

Q9UGP5 (DPOLL_HUMAN) - DNA polymerase lambda from Homo sapiens

Seq: Struc:

Seq: Struc:					575 a.a. 312 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

		C-G-G-C-C-T-T-A-C-T-G 11 bases
		C-A-G-T-A-G 6 bases
		G-C-C-G 4 bases



		Enzyme reactions

Enzyme class 2:

E.C.2.7.7.7 - DNA-directed Dna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

DNA(n)	+	2'-deoxyribonucleoside 5'-triphosphate	=	DNA(n+1)	+	diphosphate

Enzyme class 3:

E.C.4.2.99.- - ?????

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

	Proc Natl Acad Sci U S A 108:1862-1867 (2011)
PubMed id: 21233421

Replication infidelity via a mismatch with Watson-Crick geometry.
K.Bebenek, L.C.Pedersen, T.A.Kunkel.

ABSTRACT

No abstract given.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22437501

N.Demeshkina, L.Jenner, E.Westhof, M.Yusupov, and G.Yusupova (2012).
A new understanding of the decoding principle on the ribosome.

Nature, 484, 256-259.

PDB codes:

3tve 3tvf 3tvg 3tvh 3uyd 3uye 3uyf 3uyg 3uz1 3uz2 3uz3 3uz4 3uz6 3uz7 3uz8 3uz9 3uzf 3uzg 3uzh 3uzi 3uzk 3uzl 3uzm 3uzn

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.