PDBsum entry: 1huz

Transferase/DNA

PDB id: 1huz

Contents

Protein chains

325 a.a. *

DNA/RNA

Ligands

MDN ×2

Metals

_CR ×2

Waters ×122

* Residue conservation analysis

PDB id:

1huz

Name:

Transferase/DNA

Title:

Crystal structure of DNA polymerase complexed with DNA and cr-pcp

Structure:

5'-d( Ap Ap Tp Ap Gp Gp Cp Gp Tp Cp G)-3'. Chain: t, c. Engineered: yes. 5'-d(p Cp Gp Ap Cp Gp Cp Cp T)-3'. Chain: p, d. Engineered: yes. DNA polymerase beta. Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.60Å R-factor: 0.224 R-free: 0.286

Authors:

J.W.Arndt,W.Gong,X.Zhong,A.K.Showalter,J.Liu,Z.Lin,C.Paxson, M.-D.Tsai,M.K.Chan

Key ref:

J.W.Arndt et al. (2001). Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes. Biochemistry, 40, 5368-5375. PubMed id: 11330999 DOI: 10.1021/bi002176j

Date:

04-Jan-01 Release date: 23-Apr-01

Protein chains

P06766  (DPOLB_RAT) -  DNA polymerase beta

Seq: 335 a.a.

Struc: 325 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (4 terms)
• Biological process: cell death (9 terms)
• Biochemical function: catalytic activity (11 terms)

reference

DOI no: 10.1021/bi002176j

Biochemistry 40:5368-5375 (2001)

PubMed id: 11330999

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.

J.W.Arndt, W.Gong, X.Zhong, A.K.Showalter, J.Liu, C.A.Dunlap, Z.Lin, C.Paxson, M.D.Tsai, M.K.Chan.

ABSTRACT

The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA polymerase with only one metal ion bound, the DNA polymerase beta-DNA template-primer-chromium(III).2'-deoxythymidine complex, at 2.6 A resolution. The complex is distinct from the structures of other polymerase-DNA-ddNTP complexes in that the 3'-terminus of the primer has a free hydroxyl group. Hence, this structure represents a fully functional intermediate state. Support for this contention is provided by the observation of turnover in biochemical assays of crystallized protein as well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also reported. An important feature of both structures is that the fingers subdomain is closed, similar to structures of other ternary complexes in which both metal ion sites are occupied. These results suggest that closing of the fingers subdomain is induced specifically by binding of the metal-dNTP complex prior to binding of the catalytic Mg(2+) ion. This has led us to reevaluate our previous evidence regarding the existence of a rate-limiting conformational change in Pol beta's reaction pathway. The results of stopped-flow studies suggest that there is no detectable rate-limiting conformational change step.