1CLD

DNA-binding protein

• PDB DOI: https://doi.org/10.2210/pdb1CLD/pdb

• Classification: TRANSCRIPTION REGULATION
• Organism(s): Kluyveromyces lactis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-06-06 Released: 1995-09-15 
• Deposition Author(s): Gardner, K.H., Coleman, J.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 29 

Literature

Solution structure of the Kluyveromyces lactis LAC9 Cd2 Cys6 DNA-binding domain.

Gardner, K.H., Anderson, S.F., Coleman, J.E.

(1995) Nat Struct Biol 2: 898-905

• PubMed: 7552715 
• DOI: https://doi.org/10.1038/nsb1095-898
• Primary Citation of Related Structures:  
  1CLD


• PubMed Abstract: 
  

  The Zn2Cys6 DNA-binding domain has been identified by sequence homology in approximately forty fungal proteins, including the K. lactis LAC9 transcriptional activator. Using 1H NMR spectroscopy, we have determined the solution structure of a cadmium-substituted form of the LAC9 DNA-binding domain. We have complemented this approach by applying a series of 113Cd-1H NMR experiments, including several novel heteroTOCSY-based techniques. The DNA-binding domain forms a core of two alpha-helix/extended strand segments around the Cd2 binuclear cluster, with a network of amide proton-cysteinyl S gamma hydrogen bonds stabilizing the cluster. Comparison with other Zn2Cys6 domain structures provides insight into the common structural elements used in metal coordination and DNA binding.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.33 kDa 
• Atom Count: 262 
• Modelled Residue Count: 33 
• Deposited Residue Count: 61 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD2-LAC9	A	61	Kluyveromyces lactis	Mutation(s): 0
UniProt
Find proteins for P08657 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P08657  Go to UniProtKB:  P08657

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 29 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-09-15 
Deposition Author(s): Gardner, K.H., Coleman, J.E.

Revision History  

• Version 1.0: 1995-09-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection