PDBsum entry: 1t5i

Pre-mRNA processing protein

PDB id: 1t5i

Contents

Protein chain

159 a.a. *

Waters ×87

* Residue conservation analysis

PDB id:

1t5i

Name:

Pre-mRNA processing protein

Title:

Crystal structure of thE C-terminal domain of uap56

Structure:

C_terminal domain of a probable atp-dependent RNA helicase. Chain: a. Fragment: c-terminal domain (residues 259-428). Synonym: u2af65 associated protein 56, uap56. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: bat1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.224 R-free: 0.268

Authors:

R.Zhao,M.R.Green,J.Shen

Key ref:

R.Zhao et al. (2004). Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export. Structure, 12, 1373-1381. PubMed id: 15296731 DOI: 10.1016/j.str.2004.06.006

Date:

04-May-04 Release date: 31-Aug-04

Protein chain

Q13838  (DX39B_HUMAN) -  Spliceosome RNA helicase DDX39B

Seq: 428 a.a.

Struc: 159 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

reference

DOI no: 10.1016/j.str.2004.06.006

Structure 12:1373-1381 (2004)

PubMed id: 15296731

Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export.

R.Zhao, J.Shen, M.R.Green, M.MacMorris, T.Blumenthal.

ABSTRACT

UAP56 is an essential eukaryotic pre-mRNA splicing factor and mRNA export factor. The mechanisms of its functions are not well understood. We determined the crystal structures of the N- and C-terminal domains of human UAP56 (comprising 90% of the full-length UAP56) at 1.9 A resolution. The two domains each have a RecA-like fold and are connected by a flexible linker. The overall fold of each domain is highly similar to the corresponding domains of eIF4A (a prototypic DExD/H-box protein), with differences at the loops and termini. This structural similarity suggests that UAP56 is likely to possess ATPase and helicase activity similar to eIF4A. The NTP binding pocket of UAP56 is occupied by a citrate ion, mimicking the phosphates of NTP and retaining the P loop in an open conformation. The crystal structure of the N-terminal domain of UAP56 also reveals a dimer interface that is potentially important for UAP56's function.

Selected figure(s)

Figure 2.
Figure 2. Structure of UAP56 and Comparison with eIF4A(A) Structure of the N-terminal domain of UAP56 showing a typical RecA-like fold. The protein from the N terminus to the C terminus is colored from blue to red continuously in a rainbow spectrum. All figures were produced using the program PyMOL (DeLano, 2002) unless otherwise stated.(B) Superimposition of the N-terminal domains of UAP56 (cyan) and eIF4A (yellow). The overall fold is similar, but loops and termini show differences. Numbers 1 and 2 highlight two of the most different loop conformations.(C) Structure of the C-terminal domain of UAP56 showing a typical RecA-like fold. The protein from the N terminus to the C terminus is colored from blue to red continuously in a rainbow spectrum. The black dashed line represents the disordered region in the C terminus.(D) Superimposition of the C-terminal domains of UAP56 (cyan) and eIF4A (wheat). The overall fold is similar. The largest differences occur at helix a4, the a5/b6 loop (indicated by number 1), and the C termini (the blue dashed line represents the disordered region in the UAP56 C terminus). Relevant secondary structures in UAP56 are labeled in black. Wheat colored N and C represent the N terminus and C terminus of eIF4A. Cyan colored N, C, and numbers represent the N terminus, C terminus, and residue numbers in UAP56.(E) The full-length UAP56 model generated by superimposing the N-terminal and C-terminal domains on the corresponding domains in the full-length eIF4A structure. The black dashed line represents the flexible linker between the N-terminal and C-terminal domains. Conserved helicase motifs are mapped on the structure in different colors and labeled I to VI.(F) The full-length UAP56 model in a closed conformation generated by superimposing the N-terminal and C-terminal domains on the two a/b domains of HCV NS3. The dashed line represents the linker between the N-terminal and C-terminal domains. Conserved helicase motifs are mapped on the structure in different colors and labeled I to VI.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1373-1381) copyright 2004.

Figure was selected by the author.