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PDBsum entry 1odh
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protein dna_rna metals links
Transcription factor/DNA PDB id
1odh

 

 

 

 

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Contents
Protein chain
158 a.a. *
DNA/RNA
Metals
_ZN ×2
Waters ×4
* Residue conservation analysis
PDB id:
1odh
Name: Transcription factor/DNA
Title: Structure of the gcm domain bound to DNA
Structure: Mgcm1. Chain: a. Fragment: gcm domain, residues 1-174. Synonym: murine gcma (glia cell missing) transcription factor gcm1. Engineered: yes. Other_details: zn-containing DNA-binding domain. 5'-d( Cp Gp Ap Tp Gp Cp Gp Gp Gp Tp Gp Cp A)-3'. Chain: c. Synonym: DNA oligonucleotide.
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes
Biol. unit: Trimer (from PDB file)
Resolution:
2.85Å     R-factor:   0.219     R-free:   0.281
Authors: S.X.Cohen,C.W.Muller
Key ref:
S.X.Cohen et al. (2003). Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition. EMBO J, 22, 1835-1845. PubMed id: 12682016 DOI: 10.1093/emboj/cdg182
Date:
19-Feb-03     Release date:   08-Apr-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P70348  (GCM1_MOUSE) -  Chorion-specific transcription factor GCMa from Mus musculus
Seq:
Struc: 		436 a.a.
158 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  C-G-A-T-G-C-G-G-G-T-G-C-A 13 bases
  T-G-C-A-C-C-C-G-C-A-T-C-G 13 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1093/emboj/cdg182 EMBO J 22:1835-1845 (2003)
PubMed id: 12682016  
 
 
Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition.
S.X.Cohen, M.Moulin, S.Hashemolhosseini, K.Kilian, M.Wegner, C.W.Müller.
 
  ABSTRACT  
 
Glia cell missing (GCM) transcription factors form a small family of transcriptional regulators in metazoans. The prototypical Drosophila GCM protein directs the differentiation of neuron precursor cells into glia cells, whereas mammalian GCM proteins are involved in placenta and parathyroid development. GCM proteins share a highly conserved 150 amino acid residue region responsible for DNA binding, known as the GCM domain. Here we present the crystal structure of the GCM domain from murine GCMa bound to its octameric DNA target site at 2.85 A resolution. The GCM domain exhibits a novel fold consisting of two domains tethered together by one of two structural Zn ions. We observe the novel use of a beta-sheet in DNA recognition, whereby a five- stranded beta-sheet protrudes into the major groove perpendicular to the DNA axis. The structure combined with mutational analysis of the target site and of DNA-contacting residues provides insight into DNA recognition by this new type of Zn-containing DNA-binding domain.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Structure of the GCM domain. (A) Ribbon representation of the GCM domain bound to its cognate DNA. The -sheets of the large and small domains are depicted in dark blue and light blue, respectively. Helices H1, H2 and H3 are shown in red, and the DNA is shown in yellow. The two Zn ions and their coordinating ligands are depicted. Figures 2A and B, 3B, 4A and 6 were produced using the program RIBBONS (Carson, 1991). (B) View of the GCM domain with the DNA axis running vertically. DNA bases are numbered according to Figure 1B. (C) Topology diagram of the GCM domain. DNA-contacting residues and the first and second Zn ion coordinating residues are marked as dots. The color code corresponds to Figures 1A and 2A. 		Figure 3.
Figure 3 DNA recognition by the GCM domain. (A) Protein -DNA interactions between the GCM domain and its DNA target site. Arrows and dotted lines indicate polar and hydrophobic interactions, respectively. Residues involved in polar and hydrophobic interactions are drawn on blue and magenta backgrounds, respectively. (B) Ribbon representation of the interactions between the GCM domain and its DNA target site Upper and lower strands as shown in Figure 1B are depicted in yellow and orange, respectively. Broken lines indicate polar interactions.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 1835-1845) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20190276 M.R.Bowl, S.M.Mirczuk, I.V.Grigorieva, S.E.Piret, T.Cranston, L.Southam, J.Allgrove, S.Bahl, C.Brain, J.Loughlin, Z.Mughal, F.Ryan, N.Shaw, Y.V.Thakker, D.Tiosano, M.A.Nesbit, and R.V.Thakker (2010).
Identification and characterization of novel parathyroid-specific transcription factor Glial Cells Missing Homolog B (GCMB) mutations in eight families with autosomal recessive hypoparathyroidism.
  Hum Mol Genet, 19, 2028-2038.  
20144952 S.Campagne, O.Saurel, V.Gervais, and A.Milon (2010).
Structural determinants of specific DNA-recognition by the THAP zinc finger.
  Nucleic Acids Res, 38, 3466-3476.
PDB code: 2ko0
18971425 A.M.de Mestre, D.Miller, M.S.Roberson, J.Liford, L.C.Chizmar, K.E.McLaughlin, and D.F.Antczak (2009).
Glial cells missing homologue 1 is induced in differentiating equine chorionic girdle trophoblast cells.
  Biol Reprod, 80, 227-234.  
18712808 L.Canaff, X.Zhou, I.Mosesova, D.E.Cole, and G.N.Hendy (2009).
Glial cells missing-2 (GCM2) transactivates the calcium-sensing receptor gene: effect of a dominant-negative GCM2 mutant associated with autosomal dominant hypoparathyroidism.
  Hum Mutat, 30, 85-92.  
18495750 S.W.Schubert, A.Abendroth, K.Kilian, T.Vogler, B.Mayr, I.Knerr, and S.Hashemolhosseini (2008).
bZIP-Type transcription factors CREB and OASIS bind and stimulate the promoter of the mammalian transcription factor GCMa/Gcm1 in trophoblast cells.
  Nucleic Acids Res, 36, 3834-3846.  
18167345 S.W.Schubert, N.Lamoureux, K.Kilian, L.Klein-Hitpass, and S.Hashemolhosseini (2008).
Identification of integrin-alpha4, Rb1, and syncytin a as murine placental target genes of the transcription factor GCMa/Gcm1.
  J Biol Chem, 283, 5460-5465.  
17646165 C.C.Chou, C.Chang, J.H.Liu, L.F.Chen, C.D.Hsiao, and H.Chen (2007).
Small ubiquitin-like modifier modification regulates the DNA binding activity of glial cell missing Drosophila homolog a.
  J Biol Chem, 282, 27239-27249.  
17264121 M.R.Duan, J.Nan, Y.H.Liang, P.Mao, L.Lu, L.Li, C.Wei, L.Lai, Y.Li, and X.D.Su (2007).
DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein.
  Nucleic Acids Res, 35, 1145-1154.
PDB code: 2ayd
17382312 Z.Liu, S.Yu, and N.R.Manley (2007).
Gcm2 is required for the differentiation and survival of parathyroid precursor cells in the parathyroid/thymus primordia.
  Dev Biol, 305, 333-346.  
17130173 M.M.Babu, L.M.Iyer, S.Balaji, and L.Aravind (2006).
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.
  Nucleic Acids Res, 34, 6505-6520.  
15708345 A.N.Olsen, H.A.Ernst, L.L.Leggio, and K.Skriver (2005).
NAC transcription factors: structurally distinct, functionally diverse.
  Trends Plant Sci, 10, 79-87.  
16242405 C.Chotard, W.Leung, and I.Salecker (2005).
glial cells missing and gcm2 cell autonomously regulate both glial and neuronal development in the visual system of Drosophila.
  Neuron, 48, 237-251.  
15864327 C.Lin, M.Lin, and H.Chen (2005).
Biochemical characterization of the human placental transcription factor GCMa/1.
  Biochem Cell Biol, 83, 188-195.  
15640526 C.S.Yang, C.Yu, H.C.Chuang, C.W.Chang, G.D.Chang, T.P.Yao, and H.Chen (2005).
FBW2 targets GCMa to the ubiquitin-proteasome degradation system.
  J Biol Chem, 280, 10083-10090.  
16166624 C.W.Chang, H.C.Chuang, C.Yu, T.P.Yao, and H.Chen (2005).
Stimulation of GCMa transcriptional activity by cyclic AMP/protein kinase A signaling is attributed to CBP-mediated acetylation of GCMa.
  Mol Cell Biol, 25, 8401-8414.  
15721742 G.Edenfeld, T.Stork, and C.Klämbt (2005).
Neuron-glia interaction in the insect nervous system.
  Curr Opin Neurobiol, 15, 34-39.  
16240665 W.Maret (2005).
Zinc coordination environments in proteins determine zinc functions.
  J Trace Elem Med Biol, 19, 7.  
15083810 H.A.Ernst, A.N.Olsen, S.Larsen, and L.Lo Leggio (2004).
Structure of the conserved domain of ANAC, a member of the NAC family of transcription factors.
  EMBO Rep, 5, 297-303.
PDB codes: 1ut4 1ut7
15353544 S.Hashemolhosseini, and M.Wegner (2004).
Impacts of a new transcription factor family: mammalian GCM proteins in health and disease.
  J Cell Biol, 166, 765-768.  
15385555 S.W.Schubert, E.Kardash, M.A.Khan, T.Cheusova, K.Kilian, M.Wegner, and S.Hashemolhosseini (2004).
Interaction, cooperative promoter modulation, and renal colocalization of GCMa and Pitx2.
  J Biol Chem, 279, 50358-50365.  
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.

 

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