PDBsum entry 2h1k

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
Protein chains
58 a.a. *
60 a.a. *
Waters ×23
* Residue conservation analysis
PDB id:
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.
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
16-May-06     Release date:   20-Mar-07    
Go to PROCHECK summary

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 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.
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
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