Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.71 kDa 
• Atom Count: 3213 
• Residue Count: 324 
• Unique protein chains: 1

1K6X

Crystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form)

• DOI: 10.2210/pdb1K6X/pdb

• Classification: TRANSCRIPTION
• Organism(s): Aspergillus nidulans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-10-17 Released: 2002-02-20 
• Deposition Author(s): Stammers, D.K., Ren, J., Leslie, K., Nichols, C.E., Lamb, H.K., Cocklin, S., Dodds, A., Hawkins, A.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.222 
• R-Value Work: 0.189 
• R-Value Observed: 0.179 

Literature

The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases.

Stammers, D.K., Ren, J., Leslie, K., Nichols, C.E., Lamb, H.K., Cocklin, S., Dodds, A., Hawkins, A.R.

(2002) EMBO J 20: 6619-6626

• PubMed: 11726498 
• DOI: 10.1093/emboj/20.23.6619
• Primary Citation of Related Structures:  
  1K6X, 1K6J, 1K6I


• PubMed Abstract: 
  

NmrA is a negative transcriptional regulator involved in the post-translational modulation of the GATA-type transcription factor AreA, forming part of a system controlling nitrogen metabolite repression in various fungi. X-ray structures of two NmrA crystal forms, both to 1.8 A resolution, show NmrA consists of two domains, including a Rossmann fold. NmrA shows an unexpected similarity to the short-chain dehydrogenase/reductase (SDR) family, with the closest relationship to UDP-galactose 4-epimerase. We show that NAD binds to NmrA, a previously unreported nucleotide binding property for this protein. NmrA is unlikely to be an active dehydrogenase, however, as the conserved catalytic tyrosine in SDRs is absent in NmrA, and thus the nucleotide binding to NmrA could have a regulatory function. Our results suggest that other transcription factors possess the SDR fold with functions including RNA binding. The SDR fold appears to have been adapted for other roles including non-enzymatic control functions such as transcriptional regulation and is likely to be more widespread than previously recognized.

---

Related Citations: 

• Expression purification and crystallisation of Aspergillus nidulans NmrA - a negative regulatory protein involved in nitrogen metabolite repression
  Nichols, C.E., Cocklin, S., Dodds, A., Ren, J., Lamb, H., Hawkins, A.R., Stammers, D.K.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 1722

---

Organizational Affiliation: 

Structural Biology Division, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, Oxford, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NmrA	A	352	Aspergillus nidulans	Mutation(s): 0  Gene Names: nmrA
Find proteins for Q5AU62 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore Q5AU62  Go to UniProtKB:  Q5AU62

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	A	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.222 
• R-Value Work: 0.189 
• R-Value Observed: 0.179 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.69	α = 90
b = 76.69	β = 90
c = 104.48	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-10-17 
• Released Date: 2002-02-20 
Deposition Author(s): Stammers, D.K., Ren, J., Leslie, K., Nichols, C.E., Lamb, H.K., Cocklin, S., Dodds, A., Hawkins, A.R.

Revision History 

• Version 1.0: 2002-02-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model