PDBsum entry 1hqm

Transferase

PDB id: 1hqm

Contents

Protein chains

223 a.a. *

1113 a.a. *

1175 a.a. *

98 a.a. *

Metals

_ZN

_MG

* Residue conservation analysis

PDB id:

1hqm

Name:

Transferase

Title:

Crystal structure of thermus aquaticus core RNA polymerase-includes complete structure with side-chains (except for disordered regions)- further refined from original deposition-contains additional sequence information

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta. DNA-directed RNA polymerase subunit beta'.

Source:

Thermus aquaticus. Organism_taxid: 271. Organism_taxid: 271

Biol. unit:

Pentamer (from PQS)

Resolution:

3.30Å R-factor: 0.300 R-free: 0.360

Authors:

L.Minakhin,S.Bhagat,A.Brunning,E.A.Campbell,S.A.Darst,R.H.Ebright, K.Severinov

Key ref:

L.Minakhin et al. (2001). Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc Natl Acad Sci U S A, 98, 892-897. PubMed id: 11158566 DOI: 10.1073/pnas.98.3.892

Date:

18-Dec-00 Release date: 07-Feb-01

Supersedes:

1ddq

Protein chains

Q9KWU8  (RPOA_THEAQ) -  DNA-directed RNA polymerase subunit alpha from Thermus aquaticus

Seq: 314 a.a.

Struc: 223 a.a.*

Protein chain

Q9KWU7  (RPOB_THEAQ) -  DNA-directed RNA polymerase subunit beta from Thermus aquaticus

Seq: 1119 a.a.

Struc: 1113 a.a.*

Protein chain

Q9KWU6  (RPOC_THEAQ) -  DNA-directed RNA polymerase subunit beta' from Thermus aquaticus

Seq: 1524 a.a.

Struc: 1175 a.a.*

Protein chain

Q9EVV4  (RPOZ_THEAQ) -  DNA-directed RNA polymerase subunit omega from Thermus aquaticus

Seq: 99 a.a.

Struc: 98 a.a.

* PDB and UniProt seqs differ at 49 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E: 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.98.3.892

Proc Natl Acad Sci U S A 98:892-897 (2001)

PubMed id: 11158566

Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.

L.Minakhin, S.Bhagat, A.Brunning, E.A.Campbell, S.A.Darst, R.H.Ebright, K.Severinov.

ABSTRACT

Bacterial DNA-dependent RNA polymerase (RNAP) has subunit composition beta'betaalpha(I)alpha(II)omega. The role of omega has been unclear. We show that omega is homologous in sequence and structure to RPB6, an essential subunit shared in eukaryotic RNAP I, II, and III. In Escherichia coli, overproduction of omega suppresses the assembly defect caused by substitution of residue 1362 of the largest subunit of RNAP, beta'. In yeast, overproduction of RPB6 suppresses the assembly defect caused by the equivalent substitution in the largest subunit of RNAP II, RPB1. High-resolution structural analysis of the omega-beta' interface in bacterial RNAP, and comparison with the RPB6-RPB1 interface in yeast RNAP II, confirms the structural relationship and suggests a "latching" mechanism for the role of omega and RPB6 in promoting RNAP assembly.

Selected figure(s)

Figure 2.
Fig. 2. Structure determination. (a) Stereo view of a portion of the 2|F[o]| |F[c]| electron density map (3.2 Å, 1 , shown in blue) calculated from the T. aquaticus core RNAP structure, showing a region corresponding to the subunit (including the N-terminal part of CR1 -helix; at center, oriented horizontally) and nearby parts of and '. Atoms of are colored by atom type (C, yellow; O, red; N, blue; S, green). Atoms of ' and are colored pink and light blue, respectively. The SeMet difference Fourier peak (3 ) that corresponds to Met12 of is shown in magenta. Selected residues of are labeled. The figure was generated by using the program O (40). (b) Structure of the subunit in T. aquaticus RNAP core enzyme. A ribbon representation of T. aquaticus residues (residues 2-96) is shown. Residues of not included in the sequence alignment in Fig. 1 are illustrated in white; conserved regions CR1-CR3 are in yellow; nonconserved regions are in cyan. S1 is part of intersubunit -sheet (two-strand antiparallel -sheet with residues 1483-1487 of the C-terminal tail of ').

Figure 3.
Fig. 3. Bacterial and eukaryotic RPB6 are structural homologs. (a) Structure of and the - ' interface in T. aquaticus RNAP core enzyme. Residues of included in the sequence alignment in Fig. 1 are illustrated in a ribbon representation (residues 9-81); conserved regions CR1-CR3 are in yellow; nonconserved regions are in cyan. Residues of ' conserved regions D and G are in pink; residues of the ' C-terminal tail are in red, with the residue corresponding to the residue substituted in the E. coli rpoC^tsx mutant (panel f and Fig. 4a) indicated in green. (b) Location of within T. aquaticus RNAP core enzyme. The structure of T. aquaticus RNAP core enzyme is illustrated in a C representation. Conserved regions CR1-CR3 of are in yellow; nonconserved regions of are in blue; ' is in pink, with the ' C-terminal tail in red; is in cyan, I and II are in green; the active-center Mg2+ is in magenta. (c) Structure of RPB6 and the RPB6-RPB1 interface in yeast RNAP II (atomic coordinates from ref. 2, PDB accession code 1EN0, with reassignment of 79 C-terminal residues of RPB1 based on refined atomic coordinates) (P. Cramer, D. Bushnell, and R. Kornberg, personal communication). Residues of RPB6 included in the sequence alignment in Fig. 1 are illustrated in a ribbon representation (residues 80-138); conserved regions CR1-CR3 are in yellow; nonconserved regions are in cyan. Residues of RPB1 conserved regions D and G are in pink; residues of the RPB1 C-terminal tail are in red, with the residue substituted in RPB1-1 (panel f and Fig. 4b) indicated in green. (Residues of the C-terminal tail following residue Ile^1445 are not defined in the available structure.) Residue numbers in structural elements of RPB6 and RPB1 were inferred by reference to residue numbers in structurally equivalent elements of and ' (a) and to sequence alignments (Fig. 1; also panel f herein), and are expected to be correct within 1 residue. (d) Location of RPB6 within yeast RNAP II (atomic coordinates as in c). The structure of yeast RNAP II is illustrated in a C representation. Conserved regions CR1-CR3 of RPB6 are in yellow; nonconserved regions of RPB6 are in blue; RPB1 is in pink, with the RPB1 C-terminal tail in red; RPB2 is in cyan, RPB3 and RPB11 are in green; subunits of RNAP II without counterparts in bacterial RNAP (RPB5, RPB8, RPB9, RPB10, and RPB12) are in gray; the active-center Mg2+ is in magenta. (e) Structural alignment of (cyan; residues 9-81) and RPB6 (red; residues 80-138). (f) Sequences of segments of the RNAP largest subunit that interact with (a) and RBP6 (c). Conserved regions of the RNAP largest subunit are indicated by lettered boxes (8). The amino acid substitutions in E. coli rpoC^tsX and yeast RPB1-1 are indicated above the aligned sequences. Sequences shown are, in order: T. aquaticus ' (CAB65466), E. coli ' (RPOC_ECOLI), S. cerevisiae RPA1 (RPA1_YEAST), S. cerevisiae RPB1 (RPB1_YEAST), and S. cerevisiae RPC1 (RPC1_YEAST). The dots indicate amino acid identities.

Figures were selected by the author.