PDBsum entry 4a0l

Ligase/DNA-binding protein/DNA

PDB id: 4a0l

Contents

Protein chains

1105 a.a.

355 a.a.

709 a.a.

21 a.a.

DNA/RNA

PDB id:

4a0l

Name:

Ligase/DNA-binding protein/DNA

Title:

Structure of ddb1-ddb2-cul4b-rbx1 bound to a 12 bp abasic site containing DNA-duplex

Structure:

DNA damage-binding protein 1. Chain: a, c. Synonym: ddb p127 subunit, DNA damage-binding protein a, ddba, damage-specific DNA-binding protein 1, hbv x-associated protein 1, xap-1, uv-damaged DNA-binding factor, uv-damaged DNA-binding protein 1, uv-ddb 1, xpe-binding factor, xpe-bf, xeroderma pigmentosum group e-complementing protein, xpce. Engineered: yes. DNA damage-binding protein 2.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five. Danio rerio. Zebrafish. Organism_taxid: 7955.

Resolution:

7.40Å R-factor: 0.318 R-free: 0.320

Authors:

E.S.Fischer,A.Scrima,H.Gut,N.H.Thoma

Key ref:

E.S.Fischer et al. (2011). The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture, targeting, and activation. Cell, 147, 1024-1039. PubMed id: 22118460

Date:

09-Sep-11 Release date: 14-Dec-11

Protein chains

Q16531  (DDB1_HUMAN) -  DNA damage-binding protein 1 from Homo sapiens

Seq: 1140 a.a.

Struc: 1105 a.a.

Protein chains

Q2YDS1  (DDB2_DANRE) -  DNA damage-binding protein 2 from Danio rerio

Seq: 496 a.a.

Struc: 355 a.a.*

Protein chains

Q13620  (CUL4B_HUMAN) -  Cullin-4B from Homo sapiens

Seq: 913 a.a.

Struc: 709 a.a.

Protein chains

P62878  (RBX1_MOUSE) -  E3 ubiquitin-protein ligase RBX1 from Mus musculus

Seq: 108 a.a.

Struc: 21 a.a.

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

DNA/RNA chains

G-C-T-A-C-T-3DR-A-C-G-C-A 12 bases

T-G-C-G-T-A-A-G-T-A-G-C 12 bases

G-C-T-A-C-T-3DR-A-C-G-C-A 12 bases

T-G-C-G-T-A-A-G-T-A-G-C 12 bases

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D, E, H: E.C.?
• Enzyme class 3: Chains F, I: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 4: Chains F, I: E.C.2.3.2.32 - cullin-RING-type E3 NEDD8 transferase.
• Reaction: S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]- L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N₆-[NEDD8- protein]-yl-[cullin]-L-lysine

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.

Cell 147:1024-1039 (2011)

PubMed id: 22118460

The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture, targeting, and activation.

E.S.Fischer, A.Scrima, K.Böhm, S.Matsumoto, G.M.Lingaraju, M.Faty, T.Yasuda, S.Cavadini, M.Wakasugi, F.Hanaoka, S.Iwai, H.Gut, K.Sugasawa, N.H.Thomä.

ABSTRACT

No abstract given.