PDBsum entry 4u4c

Hydrolase

PDB id: 4u4c

Contents

Protein chains

924 a.a.

56 a.a.

Ligands

SO4 ×7

EDO ×2

PG4 ×2

PEG

Metals

_CL ×2

Waters ×221

PDB id:

4u4c

Name:

Hydrolase

Title:

The molecular architecture of the tramp complex reveals the organization and interplay of its two catalytic activities

Structure:

Atp-dependent RNA helicase dob1. Chain: a. Fragment: unp residues 81-1073. Synonym: mRNA transport regulator mtr4. Engineered: yes. Protein air2,poly(a) RNA polymerase protein 2. Chain: b. Fragment: unp residues 1-62,unp residues 111-160,unp residues 1-62, unp residues 111-160.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: mtr4, dob1, yjl050w, j1158. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: air2, ydl175c, pap2, trf4, yol115w, hrc584, o0716.

Resolution:

2.40Å R-factor: 0.206 R-free: 0.240

Authors:

S.Falk,J.R.Weir,J.Hentschel,P.Reichelt,F.Bonneau,E.Conti

Key ref:

S.Falk et al. (2014). The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities. Mol Cell, 55, 856-867. PubMed id: 25175027 DOI: 10.1016/j.molcel.2014.07.020

Date:

23-Jul-14 Release date: 24-Sep-14

Protein chain

P47047  (MTR4_YEAST) -  ATP-dependent RNA helicase DOB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1073 a.a.

Struc: 924 a.a.

Protein chain

P53632  (PAP2_YEAST) -  Poly(A) RNA polymerase protein 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 584 a.a.

Struc: 56 a.a.*

Protein chain

Q12476  (AIR2_YEAST) -  Protein AIR2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 344 a.a.

Struc: 56 a.a.*

* PDB and UniProt seqs differ at 46 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chain A: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 2: Chain B: E.C.2.7.7.- - ?????
• Enzyme class 3: Chain B: E.C.2.7.7.19 - polynucleotide adenylyltransferase.
• Reaction: RNA(n) + ATP = RNA(n)-3'-adenine ribonucleotide + diphosphate

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

reference

DOI no: 10.1016/j.molcel.2014.07.020

Mol Cell 55:856-867 (2014)

PubMed id: 25175027

The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities.

S.Falk, J.R.Weir, J.Hentschel, P.Reichelt, F.Bonneau, E.Conti.

ABSTRACT

The TRAMP complex is involved in the nuclear surveillance and turnover of noncoding RNAs and intergenic transcripts. TRAMP is associated with the nuclear exosome and consists of a poly(A)polymerase subcomplex (Trf4-Air2) and a helicase (Mtr4). We found that N-terminal low-complexity regions of Trf4 and Air2 bind Mtr4 in a cooperative manner. The 2.4 Å resolution crystal structure of the corresponding ternary complex reveals how Trf4 and Air2 wrap around the DExH core of the helicase. Structure-based mutations on the DExH core impair binding to Trf4 and Air2, and also to Trf5 and Air1. The combination of structural, biochemical, and biophysical data suggests that the poly(A)polymerase core of Trf4-Air2 is positioned below the base of the helicase, where the unwound 3' end of an RNA substrate is expected to emerge. The results reveal conceptual similarities between the two major regulators of the exosome, the nuclear TRAMP and cytoplasmic Ski complexes.