PDBsum entry 1ef4

Transferase

PDB id: 1ef4

Contents

Protein chain

55 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1ef4

Name:

Transferase

Title:

Solution structure of the essential RNA polymerase subunit rpb10 from methanobacterium thermoautotrophicum

Structure:

DNA-directed RNA polymerase. Chain: a. Fragment: subunit rpb10. Synonym: subunit n. Engineered: yes

Source:

Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

C.D.Mackereth,C.H.Arrowsmith,A.M.Edwards,L.P.Mcintosh,Northeast Structural Genomics Consortium (Nesg)

Key ref:

C.D.Mackereth et al. (2000). Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum. Proc Natl Acad Sci U S A, 97, 6316-6321. PubMed id: 10841539 DOI: 10.1073/pnas.97.12.6316

Date:

07-Feb-00 Release date: 14-Jun-00

Protein chain

O26147  (RPON_METTH) -  DNA-directed RNA polymerase subunit Rpo10 from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)

Seq: 55 a.a.

Struc: 55 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1073/pnas.97.12.6316

Proc Natl Acad Sci U S A 97:6316-6321 (2000)

PubMed id: 10841539

Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.

C.D.Mackereth, C.H.Arrowsmith, A.M.Edwards, L.P.McIntosh.

ABSTRACT

The RNA polymerase subunit RPB10 displays a high level of conservation across archaea and eukarya and is required for cell viability in yeast. Structure determination of this RNA polymerase subunit from Methanobacterium thermoautotrophicum reveals a topology, which we term a zinc-bundle, consisting of three alpha-helices stabilized by a zinc ion. The metal ion is bound within an atypical CX(2)CX(n)CC sequence motif and serves to bridge an N-terminal loop with helix 3. This represents an example of two adjacent zinc-binding Cys residues within an alpha-helix conformation. Conserved surface features of RPB10 include discrete regions of neutral, acidic, and basic residues, the latter being located around the zinc-binding site. One or more of these regions may contribute to the role of this subunit as a scaffold protein within the polymerase holoenzyme.

Selected figure(s)

Figure 2.
Fig. 2. NMR-derived zinc-bundle structure of mtRPB10. (A) The -trace of 20 structures of mtRBP10, superimposed by using the main chain helical atoms (14-26, 30-37, and 42-48). The helices are highlighted in red, and the zinc ion is shown as a pink ball. Every tenth residue is numbered. The N- and C-terminal residues Met1, Ile2, Glu53, Thr54, and Trp55 are conformationally flexible in solution, as evident by heteronuclear 1H{15N} NOE values less than 0.5. (B) Zinc binding site in mtRPB10. (C) Stereo view of a representative mtRPB10 structure displaying residues within the hydrophobic core: Leu7 and Val13 in the N-terminal region, Phe17, Tyr20, and Val24 of helix 1, Pro30, Val33, Leu34, and Leu37 of helix 2, Leu39 in the loop between helix 2 and 3, Leu48, Ile49 of helix 3, and Val52 in the C-terminal region. These conserved residues are shown according to the color scheme of Fig. 1.

Figure 4.
Fig. 4. Structural similarity to protein and nucleic acid binding domains. mtRPB10 is shown with helices 1, 2, and 3 colored red, green, and blue, respectively. The zinc atom is shown as a pink ball. This color scheme is used to identify similar helices in the following structurally related proteins found in the Protein Data Bank: the protein-binding N-terminal domain of HIV-2 integrase (PDB ID code 1AUB), with the zinc-chelating Cys and His residues drawn in light gray, and the zinc atom shown as a pink ball; the DNA-binding homeodomain of engrailed (PDB ID code 1ENH); and the RNA-binding domain of ribosome subunit L11 (PDB ID code 1QA6).

Figures were selected by the author.