PDBsum entry 2a8t

Translation,hydrolase

PDB id: 2a8t

Contents

Protein chains

192 a.a. *

Ligands

MGT-ADN ×2

Metals

_MN ×7

Waters ×99

* Residue conservation analysis

PDB id:

2a8t

Name:

Translation,hydrolase

Title:

2.1 angstrom crystal structure of the complex between the nuclear u8 snorna decapping nudix hydrolase x29, manganese and m7g-ppp-a

Structure:

U8 snorna-binding protein x29. Chain: a, b. Engineered: yes. Other_details: complexed with n-methyl-guanosine-triphosphate- guanosine

Source:

Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.217 R-free: 0.264

Authors:

J.N.Scarsdale,B.A.Peculis,H.T.Wright

Key ref:

J.N.Scarsdale et al. (2006). Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes. Structure, 14, 331-343. PubMed id: 16472752 DOI: 10.1016/j.str.2005.11.010

Date:

08-Jul-05 Release date: 28-Mar-06

Protein chains

Q6TEC1  (NUD16_XENLA) -  U8 snoRNA-decapping enzyme from Xenopus laevis

Seq: 212 a.a.

Struc: 192 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.6.1.62 - 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
• Reaction: a 5'-end (N₇-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O = N(7)-methyl-GDP + a 5'-end phospho-ribonucleoside in mRNA + 2 H⁺
• Enzyme class 3: E.C.3.6.1.64 - inosine diphosphate phosphatase.
• Reaction:
  1. IDP + H2O = IMP + phosphate + H⁺
  2. dIDP + H2O = dIMP + phosphate + H⁺

IDP + H2O (Bound ligand (Het Group name = MGT) matches with 84.38% similarity) = IMP + phosphate + H(+)

dIDP (Bound ligand (Het Group name = MGT) matches with 81.25% similarity) + H2O = dIMP + phosphate + H(+)

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.str.2005.11.010

Structure 14:331-343 (2006)

PubMed id: 16472752

Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes.

J.N.Scarsdale, B.A.Peculis, H.T.Wright.

ABSTRACT

X29, a 25 kDa Nudix hydrolase from Xenopus laevis that cleaves 5' caps from U8 snoRNA, crystallizes as a homodimeric apoenzyme. Manganese binds crystals of apo-X29 to form holo-X29 only in the presence of nucleot(s)ide. Structural changes in X29 on nucleo-t(s)ide-assisted Mn(+2) uptake account for the observed cooperativity of metal binding. Structures of X29 with GTP or m7GpppA show a different mode of ligand binding from that of other cap binding proteins and suggest a possible three- or four-metal Nudix reaction mechanism. The X29 dimer has no known RNA binding motif, but its striking surface dipolarity and unique structural features create a plausible RNA binding channel on the positive face of the protein. Because U8 snoRNP is essential for accumulation of mature 5.8S and 28S rRNA in vertebrate ribosome biogenesis, and cap structures are required for U8 stability in vivo, X29 could profoundly influence this fundamental cellular pathway.

Selected figure(s)

Figure 3.
Figure 3. Surface Charge Distribution of Opposite Faces of X29
Blue indicates regions of positive surface charge and red indicates negative, contoured at ± 5kt cutoff, respectively. Overlaid ribbon in (C) shows extensions (black arrow pointers) that define the two sides of the inferred RNA binding channel, which is indicated by yellow arrows. Active sites of each monomer are occupied by m7GpppA (gold and green ball-and-stick). Views are down the dyad axis.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 331-343) copyright 2006.

Figure was selected by an automated process.