PDBsum entry 1adt

DNA-binding protein

PDB id

1adt

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Contents

			Protein chain

					301 a.a. *

			Metals

					_ZN ×2

			Waters ×60

* Residue conservation analysis

Obsolete entry

PDB id:

1adt

Links

Name:

DNA-binding protein

Title:

Early e2a DNA-binding protein

Structure:

Adenovirus single-stranded DNA-binding protein. Chain: a. Fragment: c-terminal domain, residues 174 - 529. Synonym: addbp. Other_details: data collected at 295k

Source:

Human adenovirus 5. Organism_taxid: 28285. Cell: infected hela cells

Resolution:

2.60Å

R-factor:

0.197

R-free:

0.300

Authors:

P.A.Tucker,D.Tsernoglou,A.D.Tucker,H.Leenders, F.E.J.Coenjaerts,P.C.Van Der Vliet

Key ref:

P.A.Tucker et al. (1994). Crystal structure of the adenovirus DNA binding protein reveals a hook-on model for cooperative DNA binding. Embo J, 13, 2994-3002. PubMed id: 8039495

Date:

11-May-95

Release date:

20-Jun-96

PROCHECK

	Headers

	References

Protein chain

P03265 (DNB2_ADE05) - DNA-binding protein from Human adenovirus C serotype 5

Seq: Struc:

Seq: Struc:					529 a.a. 301 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

	Embo J 13:2994-3002 (1994)
PubMed id: 8039495

Crystal structure of the adenovirus DNA binding protein reveals a hook-on model for cooperative DNA binding.
P.A.Tucker, D.Tsernoglou, A.D.Tucker, F.E.Coenjaerts, H.Leenders, P.C.van der Vliet.

ABSTRACT

The adenovirus single-stranded DNA binding protein (Ad DBP) is a multifunctional protein required, amongst other things, for DNA replication and transcription control. It binds to single- and double-stranded DNA, as well as to RNA, in a sequence-independent manner. Like other single-stranded DNA binding proteins, it binds ssDNA, cooperatively. We report the crystal structure, at 2.6 A resolution, of the nucleic acid binding domain. This domain is active in DNA replication. The protein contains two zinc atoms in different, novel coordinations. The zinc atoms appear to be required for the stability of the protein fold rather than being involved in direct contacts with the DNA. The crystal structure shows that the protein contains a 17 amino acid C-terminal extension which hooks onto a second molecule, thereby forming a protein chain. Deletion of this C-terminal arm reduces cooperativity in DNA binding, suggesting a hook-on model for cooperativity. Based on this structural work and mutant studies, we propose that DBP forms a protein core around which the single-stranded DNA winds.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18065449

G.Witte, R.Fedorov, and U.Curth (2008).
Biophysical analysis of Thermus aquaticus single-stranded DNA binding protein.

Biophys J, 94, 2269-2279.

18678909

O.Dym, S.Albeck, T.Unger, J.Jacobovitch, A.Branzburg, Y.Michael, D.Frenkiel-Krispin, S.G.Wolf, and M.Elbaum (2008).
Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners.

Proc Natl Acad Sci U S A, 105, 11170-11175.

PDB code:

3btp

17928348

J.York, and J.H.Nunberg (2007).
A novel zinc-binding domain is essential for formation of the functional Junín virus envelope glycoprotein complex.

J Virol, 81, 13385-13391.

15671019

J.B.Robbins, M.C.McKinney, C.E.Guzman, B.Sriratana, S.Fitz-Gibbon, T.Ha, and I.K.Cann (2005).
The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins.

J Biol Chem, 280, 15325-15339.

15531602

M.M.Gromiha, and M.Suwa (2005).
A simple statistical method for discriminating outer membrane proteins with better accuracy.

Bioinformatics, 21, 961-968.

15507432

M.Mapelli, S.Panjikar, and P.A.Tucker (2005).
The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding.

J Biol Chem, 280, 2990-2997.

PDB code:

1urj

12502807

B.van Breukelen, A.B.Brenkman, P.E.Holthuizen, and P.C.van der Vliet (2003).
Adenovirus type 5 DNA binding protein stimulates binding of DNA polymerase to the replication origin.

J Virol, 77, 915-922.

12228710

H.Yang, P.D.Jeffrey, J.Miller, E.Kinnucan, Y.Sun, N.H.Thoma, N.Zheng, P.L.Chen, W.H.Lee, and N.P.Pavletich (2002).
BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.

Science, 297, 1837-1848.

PDB codes:

1iyj 1miu 1mje

11956216

I.Gascón, J.L.Carrascosa, L.Villar, J.M.Lázaro, and M.Salas (2002).
Importance of the N-terminal region of the phage GA-1 single-stranded DNA-binding protein for its self-interaction ability and functionality.

J Biol Chem, 277, 22534-22540.

10773070

I.Gascón, J.M.Lázaro, and M.Salas (2000).
Differential functional behavior of viral phi29, Nf and GA-1 SSB proteins.

Nucleic Acids Res, 28, 2034-2042.

10712935

J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.

Chem Biol, 7, R63-R71.

10982323

M.Mapelli, M.Mühleisen, G.Persico, H.van Der Zandt, and P.A.Tucker (2000).
The 60-residue C-terminal region of the single-stranded DNA binding protein of herpes simplex virus type 1 is required for cooperative DNA binding.

J Virol, 74, 8812-8822.

9469832

E.J.Parker, C.H.Botting, A.Webster, and R.T.Hay (1998).
Adenovirus DNA polymerase: domain organisation and interaction with preterminal protein.

Nucleic Acids Res, 26, 1240-1247.

9445040

P.S.Reddy, N.Idamakanti, A.N.Zakhartchouk, M.K.Baxi, J.B.Lee, C.Pyne, L.A.Babiuk, and S.K.Tikoo (1998).
Nucleotide sequence, genome organization, and transcription map of bovine adenovirus type 3.

J Virol, 72, 1394-1402.

9819409

S.J.Brill, and S.Bastin-Shanower (1998).
Identification and characterization of the fourth single-stranded-DNA binding domain of replication protein A.

Mol Cell Biol, 18, 7225-7234.

8985382

A.Webster, I.R.Leith, and R.T.Hay (1997).
Domain organization of the adenovirus preterminal protein.

J Virol, 71, 539-547.

9164449

D.Suck (1997).
Common fold, common function, common origin?

Nat Struct Biol, 4, 161-165.

9013582

H.C.van Leeuwen, M.Rensen, and P.C.van der Vliet (1997).
The Oct-1 POU homeodomain stabilizes the adenovirus preinitiation complex via a direct interaction with the priming protein and is displaced when the replication fork passes.

J Biol Chem, 272, 3398-3405.

9135160

J.Dekker, P.N.Kanellopoulos, A.K.Loonstra, J.A.van Oosterhout, K.Leonard, P.A.Tucker, and P.C.van der Vliet (1997).
Multimerization of the adenovirus DNA-binding protein is the driving force for ATP-independent DNA unwinding during strand displacement synthesis.

EMBO J, 16, 1455-1463.

8995262

M.S.Soengas, C.R.Mateo, G.Rivas, M.Salas, A.U.Acuña, and C.Gutiérrez (1997).
Structural features of phi29 single-stranded DNA-binding protein. II. Global conformation of phi29 single-stranded DNA-binding protein and the effects of complex formation on the protein and the single-stranded DNA.

J Biol Chem, 272, 303-310.

9230044

R.H.Folmer, M.Nilges, C.H.Papavoine, B.J.Harmsen, R.N.Konings, and C.W.Hilbers (1997).
Refined structure, DNA binding studies, and dynamics of the bacteriophage Pf3 encoded single-stranded DNA binding protein.

Biochemistry, 36, 9120-9135.

8612277

A.E.Hodel, P.D.Gershon, X.Shi, and F.A.Quiocho (1996).
The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.

Cell, 85, 247-256.

PDB code:

1vpt

8910351

J.L.Villemain, and D.P.Giedroc (1996).
Characterization of a cooperativity domain mutant Lys3 --> Ala (K3A) T4 gene 32 protein.

J Biol Chem, 271, 27623-27629.

8523532

K.Watanabe, H.Handa, K.Mizumoto, and K.Nagata (1996).
Mechanism for inhibition of influenza virus RNA polymerase activity by matrix protein.

J Virol, 70, 241-247.

8756638

L.J.Blackwell, J.A.Borowiec, and I.A.Mastrangelo (1996).
Single-stranded-DNA binding alters human replication protein A structure and facilitates interaction with DNA-dependent protein kinase.

Mol Cell Biol, 16, 4798-4807.

8994967

T.S.Peat, E.G.Frank, J.P.McDonald, A.S.Levine, R.Woodgate, and W.A.Hendrickson (1996).
The UmuD' protein filament and its potential role in damage induced mutagenesis.

Structure, 4, 1401-1412.

PDB code:

1ay9

7556054

R.H.Folmer, M.Nilges, R.N.Konings, and C.W.Hilbers (1995).
Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.

EMBO J, 14, 4132-4142.

PDB code:

1pfs

7565651

A.P.Stassen, R.H.Folmer, C.W.Hilbers, and R.N.Konings (1994).
Single-stranded DNA binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics.

Mol Biol Rep, 20, 109-127.

7966622

D.C.Zijderveld, F.d'Adda di Fagagna, M.Giacca, H.T.Timmers, and P.C.van der Vliet (1994).
Stimulation of the adenovirus major late promoter in vitro by transcription factor USF is enhanced by the adenovirus DNA binding protein.

J Virol, 68, 8288-8295.

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.