PDBsum entry: 2vus

Transcription

PDB-id: 2vus

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

318 a.a. *

42 a.a. *

43 a.a. *

Ligands

SO4 ×8

Metal ions

_CL ×7

_ZN ×8

Waters ×1612

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

2vus

Name:

Transcription

Title:

Crystal structure of unliganded nmra-area zinc finger complex

Structure:

Nitrogen metabolite repression regulator nmra. Chain: a, b, c, d, e, f, g, h. Synonym: nmra. Engineered: yes. Nitrogen regulatory protein area. Chain: i, j, k, l, m, n, o, p. Fragment: zinc finger domain, residues 670-712. Synonym: area. Engineered: yes

Source:

Emericella nidulans. Organism_taxid: 162425. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_taxid: 511693.

UniProt:

Chains A, B, C, D, E, F, G, H: O59919 (O59919_EMENI)

Seq:
Struc:
	Seq:	352 a.a.
	Struc:	318 a.a.*

Chains I, J, K, L: P17429 (AREA_EMENI)

Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:	876 a.a.
	Struc:	42 a.a.

Chains M, N, O, P: P17429 (AREA_EMENI)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

876 a.a.

Struc:

43 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

2.60Å

R-factor:

0.242

R-free:

0.306

Authors:

M.Kotaka,C.Johnson,H.K.Lamb,A.R.Hawkins,J.Ren,D.K.Stammers

Key ref:

M.Kotaka et al. (2008). Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA.. J Mol Biol, 381, 373-382. [PubMed id: 18602114] [DOI: 10.1016/j.jmb.2008.05.077]

Date:

30-May-08

Release date:

29-Jul-08

Related entries:

2vut crystal structure of NAD-bound nmra-area zinc finger complex
2vuu crystal structure of NADP-bound nmra-area zinc finger complex

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Key reference

DOI no: 10.1016/j.jmb.2008.05.077

J Mol Biol 381:373-382 (2008)

PubMed id: 18602114

Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA.

M.Kotaka, C.Johnson, H.K.Lamb, A.R.Hawkins, J.Ren, D.K.Stammers.

ABSTRACT

Amongst the most common protein motifs in eukaryotes are zinc fingers (ZFs), which, although largely known as DNA binding modules, also can have additional important regulatory roles in forming protein:protein interactions. AreA is a transcriptional activator central to nitrogen metabolism in Aspergillus nidulans. AreA contains a GATA-type ZF that has a competing dual recognition function, binding either DNA or the negative regulator NmrA. We report the crystal structures of three AreA ZF-NmrA complexes including two with bound NAD(+) or NADP(+). The molecular recognition of AreA ZF-NmrA involves binding of the ZF to NmrA via hydrophobic and hydrogen bonding interactions through helices alpha1, alpha6 and alpha11. Comparison with an earlier NMR solution structure of AreA ZF-DNA complex by overlap of the AreA ZFs shows that parts of helices alpha6 and alpha11 of NmrA are positioned close to the GATA motif of the DNA, mimicking the major groove of DNA. The extensive overlap of DNA with NmrA explains their mutually exclusive binding to the AreA ZF. The presence of bound NAD(+)/NADP(+) in the NmrA-AreaA ZF complex, however, causes minimal structural changes. Thus, any regulatory effects on AreA function mediated by the binding of oxidised nicotinamide dinucleotides to NmrA in the NmrA-AreA ZF complex appear not to be modulated via protein conformational rearrangements.

Selected figure(s)

Figure 1.
Fig. 1. (a) Orthogonal views of the NmrA–AreA ZF complex in stereo. NmrA (white) is shown with NAD^+ bound. AreA ZF is shown in red, and the α-helices of NmrA involved in AreA interaction are highlighted in yellow and labelled. (b) Simulated annealing omit difference map of residues 702 to 712 of AreA ZF at σ = 2.5. The carbon atoms are drawn in black.

Figure 2.
Fig. 2. Stereo representations of the NmrA–AreA ZF binding interface. (a) Interaction between the C-terminal tail of AreA ZF (cyan) and NmrA helix α6 (yellow). (b) Interaction between the AreA ZF protein core (cyan) and NmrA helix α11 (yellow).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 373-382) copyright 2008.

Figures were selected by an automated process.