PDBsum entry: 1aro

Complex (polymerase/hydrolase)

PDB id: 1aro

Contents

Protein chains

774 a.a. *

149 a.a. *

Metals

_HG ×7

* Residue conservation analysis

PDB id:

1aro

Name:

Complex (polymerase/hydrolase)

Title:

T7 RNA polymerase complexed with t7 lysozyme

Structure:

T7 RNA polymerase. Chain: p. Engineered: yes. Mutation: yes. T7 lysozyme. Chain: l. Synonym: n-acetylmuramoyl-l-alanine amidase. Engineered: yes

Source:

Enterobacteria phage t7. Organism_taxid: 10760. Gene: t7. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Monomer (from PDB file)

Resolution:

2.80Å R-factor: 0.262 R-free: 0.309

Authors:

T.Steitz,D.Jeruzalmi

Key ref:

D.Jeruzalmi and T.A.Steitz (1998). Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J, 17, 4101-4113. PubMed id: 9670025 DOI: 10.1093/emboj/17.14.4101

Date:

08-Aug-97 Release date: 21-Oct-98

Protein chain

P00573  (RPOL_BPT7) -  DNA-directed RNA polymerase

Seq: 883 a.a.

Struc: 774 a.a.*

Protein chain

P00806  (NAAA_BPT7) -  N-acetylmuramoyl-L-alanine amidase

Seq: 151 a.a.

Struc: 149 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain L: E.C.3.5.1.28 - N-acetylmuramoyl-L-alanine amidase.
• Reaction: Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
• Enzyme class 3: Chain P: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)

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

 Gene Ontology (GO) functional annotation 

• Biological process: peptidoglycan catabolic process (2 terms)
• Biochemical function: protein binding (8 terms)

reference

DOI no: 10.1093/emboj/17.14.4101

EMBO J 17:4101-4113 (1998)

PubMed id: 9670025

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.

D.Jeruzalmi, T.A.Steitz.

ABSTRACT

The T7 RNA polymerase-T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 A crystal structure of the complex reveals that lysozyme binds at a site remote from the polymerase active site, suggesting an indirect mechanism of inhibition. Comparison of the T7 RNA polymerase structure with that of the homologous pol I family of DNA polymerases reveals identities in the catalytic site but also differences specific to RNA polymerase function. The structure of T7 RNA polymerase presented here differs significantly from a previously published structure. Sequence similarities between phage RNA polymerases and those from mitochondria and chloroplasts, when interpreted in the context of our revised model of T7 RNA polymerase, suggest a conserved fold.

Selected figure(s)

Figure 2.
Figure 2 Representative electron density maps. (A) Residues 734 -739 of an intermediate model of the PL complex are superimposed onto the final 4-fold domain averaged electron density map (20 -3.0 Å) in crystal form III. The map is contoured at 1.3 . (B) An annealed 2F[o]-F[c] omit electron density map, calculated by excluding residues 734 -739 of the final PL complex model. The map is contoured at 1.3 .

Figure 6.
Figure 6 Model for interaction with promoter DNA and nascent RNA. (A) RNAP is represented as a molecular surface, colored by domain as in Figure 1, showing the highly concave shape of its active-site cleft. The 'pinky' specificity loop is depicted as a light blue ribbon of connected C[ ]atoms. The nucleic acid duplex present in the RNAP cleft is represented as a ribbon (RNA, brown; DNA, magenta), corresponding to the phosphodiester backbone, with cylinders as bases. Its location derives from super-position of the three -strands from the active site from the Taq DNA polymerase -duplex DNA complex (Eom et al., 1996). Of the 14/15mer duplex present in the DNA polymerase structure, 6 -8 bases can be accomodated in the cleft of RNAP. (B) A close-up view of the active-site cleft found in RNAP with the modeled nucleic acid duplex showing clashes with the N-terminal domain. This view of RNAP is identical to (A) except that -helices are depicted as tubes, -strands as arrows. Helices F, G and the adjoining loop (N-terminal domain) are colored yellow, the active-site -strands are in red and the specificity loop is colored light blue. For clarity, the remaining portions of the RNAP structure are colored grey. The position of residues significant for rNTP binding (GLY542), catalysis (ASP812), promoter interaction (ASN 748) are indicated. The location of GLU148, a residue whose mutation severely disrupts RNA binding and processivity (He et al., 1997) is highlighted. (C) The DNA polymerase from Thermus aquaticus is represented as molecular surface showing its more open active-site cleft. The surface is colored as in (A). The vestigial 3'-5' exonuclease domain is colored in white. For clarity, the 5' exo-nuclease domain has been deleted. The DNA from the complex is modeled and colored as in (B).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 4101-4113) copyright 1998.

Figures were selected by an automated process.