PDBsum entry 3odc

DNA binding protein/DNA

PDB id

3odc

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Contents

			Protein chains

					93 a.a. *


					100 a.a. *

			DNA/RNA

			Metals

					_ZN ×2

			Waters ×39

* Residue conservation analysis

PDB id:

3odc

Links

Name:

DNA binding protein/DNA

Title:

Human parp-1 zinc finger 2 (zn2) bound to DNA

Structure:

Poly [adp-ribose] polymerase 1. Chain: a, b. Fragment: parp-1 zinc finger 2, zn2, unp residues 105-206. Synonym: parp-1, NAD(+) adp-ribosyltransferase 1, adprt 1, poly[adp- ribose] synthase 1. Engineered: yes. 5'-d( Cp Cp Cp Ap Gp Ap Cp G)-3'. Chain: c, e. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: adprt, parp1, ppol. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: chemically synthesized DNA. Other_details: chemically synthesized DNA

Resolution:

2.80Å

R-factor:

0.195

R-free:

0.240

Authors:

J.M.Pascal,M.-F.Langelier

Key ref:

M.F.Langelier et al. (2011). Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity. J Biol Chem, 286, 10690-10701. PubMed id: 21233213

Date:

11-Aug-10

Release date:

12-Jan-11

PROCHECK

	Headers

	References

Protein chain

P09874 (PARP1_HUMAN) - Poly [ADP-ribose] polymerase 1 from Homo sapiens

Seq: Struc:

Seq: Struc:					1014 a.a. 93 a.a.

Protein chain

P09874 (PARP1_HUMAN) - Poly [ADP-ribose] polymerase 1 from Homo sapiens

Seq: Struc:

Seq: Struc:					1014 a.a. 100 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

		C-C-C-A-G-A-C-G 8 bases
		C-G-T-C-T-G-G-G 8 bases
		C-C-C-A-G-A-C-G 8 bases
		C-G-T-C-T-G-G-G 8 bases



		Enzyme reactions

Enzyme class 1:

Chains A, B: E.C.2.4.2.- - ?????

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

Enzyme class 2:

Chains A, B: E.C.2.4.2.30 - NAD(+) ADP-ribosyltransferase.

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

Pathway:

Reaction:

NAD⁺ + (ADP-D-ribosyl)n-acceptor = nicotinamide + (ADP-D- ribosyl)n+1-acceptor + H⁺

NAD(+)	+	(ADP-D-ribosyl)n-acceptor	=	nicotinamide	+	(ADP-D- ribosyl)n+1-acceptor	+	H(+)

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

	J Biol Chem 286:10690-10701 (2011)
PubMed id: 21233213

Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity.
M.F.Langelier, J.L.Planck, S.Roy, J.M.Pascal.

ABSTRACT

No abstract given.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22683995

A.A.Ali, G.Timinszky, R.Arribas-Bosacoma, M.Kozlowski, P.O.Hassa, M.Hassler, A.G.Ladurner, L.H.Pearl, and A.W.Oliver (2012).
The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks.

Nat Struct Mol Biol, 19, 685-692.

PDB code:

4av1

22713970

B.A.Gibson, and W.L.Kraus (2012).
New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.

Nat Rev Mol Cell Biol, 13, 411-424.

22767236

N.Coquelle, and J.N.Glover (2012).
PARP pairs up to PARsylate.

Nat Struct Mol Biol, 19, 660-661.

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 code is shown on the right.