PDBsum entry: 2pmz

Translation, transferase

PDB id: 2pmz

Contents

Protein chains

776 a.a. *

279 a.a. *

1090 a.a. *

264 a.a. *

176 a.a. *

89 a.a. *

74 a.a. *

82 a.a. *

92 a.a. *

64 a.a. *

43 a.a. *

Ligands

F3S ×2

Metals

_MG ×2

_ZN ×8

* Residue conservation analysis

PDB id:

2pmz

Name:

Translation, transferase

Title:

Archaeal RNA polymerase from sulfolobus solfataricus

Structure:

DNA-directed RNA polymerase subunit a. Chain: a, q. DNA-directed RNA polymerase subunit a". Chain: c, g. DNA-directed RNA polymerase subunit b. Chain: b, r. DNA-directed RNA polymerase subunit d. Chain: d, s. DNA-directed RNA polymerase subunit e.

Source:

Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Strain: p2

Resolution:

3.40Å R-factor: 0.274 R-free: 0.343

Authors:

K.S.Murakami

Key ref:

A.Hirata et al. (2008). The X-ray crystal structure of RNA polymerase from Archaea. Nature, 451, 851-854. PubMed id: 18235446 DOI: 10.1038/nature06530

Date:

23-Apr-07 Release date: 12-Feb-08

Protein chains

Q980R2  (RPOA1_SULSO) -  DNA-directed RNA polymerase subunit A'

Seq: 880 a.a.

Struc: 776 a.a.

Protein chains

P58192  (RPOA2_SULSO) -  DNA-directed RNA polymerase subunit A''

Seq: 392 a.a.

Struc: 279 a.a.

Protein chains

Q980R1  (Q980R1_SULSO) -  DNA-directed RNA polymerase

Seq: 649 a.a.

Struc: 1090 a.a.*

Protein chains

P95989  (RPOD_SULSO) -  DNA-directed RNA polymerase subunit D

Seq: 265 a.a.

Struc: 264 a.a.

Protein chains

Q980A3  (Q980A3_SULSO) -  DNA-directed RNA polymerase, subunit E' (RpoE1)

Seq: 180 a.a.

Struc: 176 a.a.

Protein chains

Q9UXD9  (Q9UXD9_SULSF) -  Putative uncharacterized protein ORF-c20_042

Seq: 113 a.a.

Struc: 89 a.a.

Protein chains

Q980Q9  (RPOH_SULSO) -  DNA-directed RNA polymerase subunit H

Seq: 84 a.a.

Struc: 74 a.a.

Protein chains

Q97ZJ9  (RPOK_SULSO) -  DNA-directed RNA polymerase subunit K

Seq: 95 a.a.

Struc: 82 a.a.

Protein chains

Q980K0  (RPOL_SULSO) -  DNA-directed RNA polymerase subunit L

Seq: 92 a.a.

Struc: 92 a.a.

Protein chains

Q980Z8  (RPON_SULSO) -  DNA-directed RNA polymerase subunit N

Seq: 66 a.a.

Struc: 64 a.a.

Protein chains

Q97ZX7  (RPOP_SULSO) -  DNA-directed RNA polymerase subunit P

Seq: 48 a.a.

Struc: 43 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C, B, D, E, H, K, L, N, P, Q, G, R, S, T, V, W, X, Y, Z: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: RNA polymerase complex (1 term)
• Biological process: cellular metabolic process (3 terms)
• Biochemical function: catalytic activity (11 terms)

reference

DOI no: 10.1038/nature06530

Nature 451:851-854 (2008)

PubMed id: 18235446

The X-ray crystal structure of RNA polymerase from Archaea.

A.Hirata, B.J.Klein, K.S.Murakami.

ABSTRACT

The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase (RNAP) II counterpart, comprising an RNAPII-like enzyme as well as two general transcription factors, the TATA-binding protein (TBP) and the eukaryotic TFIIB orthologue TFB. It has been widely understood that precise comparisons of cellular RNAP crystal structures could reveal structural elements common to all enzymes and that these insights would be useful in analysing components of each enzyme that enable it to perform domain-specific gene expression. However, the structure of archaeal RNAP has been limited to individual subunits. Here we report the first crystal structure of the archaeal RNAP from Sulfolobus solfataricus at 3.4 A resolution, completing the suite of multi-subunit RNAP structures from all three domains of life. We also report the high-resolution (at 1.76 A) crystal structure of the D/L subcomplex of archaeal RNAP and provide the first experimental evidence of any RNAP possessing an iron-sulphur (Fe-S) cluster, which may play a structural role in a key subunit of RNAP assembly. The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription.

Selected figure(s)

Figure 2.
Figure 2: Cellular RNAP structures from three domains of life. Surface representations of multi-subunit cellular RNAP structures from Bacteria (left, T. aquaticus core enzyme^30), Archaea (centre, S. solfataricus) and Eukarya (right, Saccharomyces cerevisiae RNAPII^13). Each subunit is denoted by a unique colour and labelled. Orthologous subunits are depicted by the same colour.

Figure 3.
Figure 3: Structures around the foot domains from three domains of life. a, Ribbon model of the archaeal RNAP (the colour coding of each subunit is indicated). Various domains and motifs are labelled. The junction between A' and A'' is positioned at the foot domain. Subunits H and K associate around the base of the foot. b, Ribbon model of the eukaryotic RNAPII^13. The same four -helix architecture, which is found in the archaeal RNAP, is conserved in the centre of the RNAPII foot domain. Rpb5 and Rpb6 also associate around the foot domain. c, Ribbon model of the bacterial RNAP^30. The bacterial foot domain has a completely different architecture. The right side of the bacterial foot domain associates with the bacterial-specific insertion of the ' subunit. In addition, the tail wraps around the C terminus of the ' subunit.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2008, 451, 851-854) copyright 2008.

Figures were selected by the author.