spacer
spacer

PDBsum entry 2h1k

Go to PDB code: 
protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
2h1k
Jmol
Contents
Protein chains
58 a.a. *
60 a.a. *
DNA/RNA
Waters ×23
* Residue conservation analysis
PDB id:
2h1k
Name: Transcription/DNA
Title: Crystal structure of the pdx1 homeodomain in complex with DNA
Structure: 15-mer DNA. Chain: c, e. Engineered: yes. 15-mer DNA. Chain: d, f. Engineered: yes. Pancreatic and duodenal homeobox 1. Chain: a, b. Fragment: residues 146-206.
Source: Synthetic: yes. Mesocricetus auratus. Golden hamster. Organism_taxid: 10036. Gene: ipf1, pdx1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.42Å     R-factor:   0.227     R-free:   0.277
Authors: A.Longo,G.P.Guanga,R.B.Rose
Key ref:
A.Longo et al. (2007). Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain. Biochemistry, 46, 2948-2957. PubMed id: 17315980 DOI: 10.1021/bi060969l
Date:
16-May-06     Release date:   20-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P70118  (PDX1_MESAU) -  Pancreas/duodenum homeobox protein 1
Seq:
Struc:
283 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P70118  (PDX1_MESAU) -  Pancreas/duodenum homeobox protein 1
Seq:
Struc:
283 a.a.
60 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1021/bi060969l Biochemistry 46:2948-2957 (2007)
PubMed id: 17315980  
 
 
Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain.
A.Longo, G.P.Guanga, R.B.Rose.
 
  ABSTRACT  
 
Pancreatic and duodenal homeobox 1 (Pdx1) is a homeodomain transcription factor belonging to the ParaHox family. Pdx1 plays an essential role in pancreatic endocrine and exocrine cell development and maintenance of adult islet beta-cell function. Mutations in the human pdx1 gene are linked to an early onset form of non-insulin-dependent diabetes mellitus, MODY-4. We demonstrate that the homeodomain reproduces the binding specificity of the full-length protein. We report the 2.4 A resolution crystal structure of the homeodomain bound to a target DNA. The two Pdx1/DNA complexes in the asymmetric unit display conformational differences: in the DNA curvature, the orientation of the homeodomain in the major groove, and the order of the N-terminal arm. Comparing the two complexes indicates invariant protein-DNA contacts, and variant contacts that are unique to each binding orientation. An induced fit model is proposed that depends on the DNA conformation and provides a mechanism for nonlocal contributions to binding specificity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18698640 A.Moussa, C.Pham, S.Bommireddy, and G.Muller (2009).
Importance of hydrogen-bonding sites in the chiral recognition mechanism between racemic D3 terbium(III) complexes and amino acids.
  Chirality, 21, 497-506.  
20067590 E.van der Graaff, T.Laux, and S.A.Rensing (2009).
The WUS homeobox-containing (WOX) protein family.
  Genome Biol, 10, 248.  
17659992 D.A.Babu, T.G.Deering, and R.G.Mirmira (2007).
A feat of metabolic proportions: Pdx1 orchestrates islet development and function in the maintenance of glucose homeostasis.
  Mol Genet Metab, 92, 43-55.  
17576674 J.Boudet, V.Duval, H.Van Melckebeke, M.Blackledge, A.Amoroso, B.Joris, and J.P.Simorre (2007).
Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against beta-lactam antibiotics.
  Nucleic Acids Res, 35, 4384-4395.
PDB code: 2p7c
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.