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PDBsum entry 1ruo
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protein dna_rna ligands Protein-protein interface(s) links
Transcription/DNA PDB id
1ruo

 

 

 

 

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Contents
Protein chains
198 a.a. *
DNA/RNA
Ligands
CMP ×2
Waters ×35
* Residue conservation analysis
PDB id:
1ruo
Name: Transcription/DNA
Title: Catabolite gene activator protein (cap) mutant/DNA complex + adenosine-3',5'-cyclic-monophosphate
Structure: DNA (5'-d( Gp Cp Gp Ap Ap Ap Ap Ap Tp Gp Tp Gp Ap T)-3'). Chain: c, e. Engineered: yes. DNA (5'- d( Cp Tp Ap Gp Ap Tp Cp Ap Cp Ap Tp Tp Tp Tp Tp Cp G )-3'). Chain: d, f. Engineered: yes. Protein (catabolite gene activator protein (cap)). Chain: a, b.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.70Å     R-factor:   0.213    
Authors: G.N.Parkinson,R.H.Ebright,H.M.Berman
Key ref: G.Parkinson et al. (1996). Aromatic hydrogen bond in sequence-specific protein DNA recognition. Nat Struct Biol, 3, 837-841. PubMed id: 8836098
Date:
26-May-96     Release date:   10-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ACJ8  (CRP_ECOLI) -  DNA-binding transcriptional dual regulator CRP from Escherichia coli (strain K12)
Seq:
Struc: 		210 a.a.
198 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  G-C-G-A-A-A-A-A-T-G-T-G-A-T 14 bases
  C-T-A-G-A-T-C-A-C-A-T-T-T-T-T-C-G 17 bases
  G-C-G-A-A-A-A-A-T-G-T-G-A-T 14 bases
  C-T-A-G-A-T-C-A-C-A-T-T-T-T-T-C-G 17 bases

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

 

 
Nat Struct Biol 3:837-841 (1996)
PubMed id: 8836098  
 
 
Aromatic hydrogen bond in sequence-specific protein DNA recognition.
G.Parkinson, A.Gunasekera, J.Vojtechovsky, X.Zhang, T.A.Kunkel, H.Berman, R.H.Ebright.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265791 G.Giardina, N.Castiglione, M.Caruso, F.Cutruzzolà, and S.Rinaldo (2011).
The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms.
  Biochem Soc Trans, 39, 294-298.  
21541844 K.Ramanathan, V.Shanthi, and R.Sethumadhavan (2011).
A compact review on the comparison of conventional and non-conventional interactions on the structural stability of therapeutic proteins.
  Interdiscip Sci, 3, 144-160.  
20525797 C.Y.Wu, Y.C.Chen, and C.Lim (2010).
A structural-alphabet-based strategy for finding structural motifs across protein families.
  Nucleic Acids Res, 38, e150.  
19415759 G.Giardina, S.Rinaldo, N.Castiglione, M.Caruso, and F.Cutruzzolà (2009).
A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.
  Proteins, 77, 174-180.
PDB code: 3dkw
17219397 C.M.Baker, and G.H.Grant (2007).
Role of aromatic amino acids in protein-nucleic acid recognition.
  Biopolymers, 85, 456-470.  
17526705 R.S.De Silva, G.Kovacikova, W.Lin, R.K.Taylor, K.Skorupski, and F.J.Kull (2007).
Crystal structure of the Vibrio cholerae quorum-sensing regulatory protein HapR.
  J Bacteriol, 189, 5683-5691.
PDB code: 2pbx
16427082 A.A.Napoli, C.L.Lawson, R.H.Ebright, and H.M.Berman (2006).
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
  J Mol Biol, 357, 173-183.
PDB codes: 1zrc 1zrd 1zre 1zrf
16586530 K.Fukuzawa, Y.Komeiji, Y.Mochizuki, A.Kato, T.Nakano, and S.Tanaka (2006).
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: ab initio fragment molecular orbital study.
  J Comput Chem, 27, 948-960.  
16835922 S.Chakkaravarthi, M.M.Babu, M.M.Gromiha, G.Jayaraman, and R.Sethumadhavan (2006).
Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins.
  Proteins, 65, 75-86.  
15102444 C.L.Lawson, D.Swigon, K.S.Murakami, S.A.Darst, H.M.Berman, and R.H.Ebright (2004).
Catabolite activator protein: DNA binding and transcription activation.
  Curr Opin Struct Biol, 14, 10-20.  
15173120 G.E.Crooks, G.Hon, J.M.Chandonia, and S.E.Brenner (2004).
WebLogo: a sequence logo generator.
  Genome Res, 14, 1188-1190.  
15557262 G.Spraggon, D.Pantazatos, H.E.Klock, I.A.Wilson, V.L.Woods, and S.A.Lesley (2004).
On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171.
  Protein Sci, 13, 3187-3199.
PDB codes: 1o5l 1sj5 1vjl
15103140 S.Wisén, T.Sjögren, B.Olin, and B.Mannervik (2004).
Purification, crystallization and preliminary X-ray data of the transcription factor NtcA from the cyanobacterium Anabaena PCC 7120.
  Acta Crystallogr D Biol Crystallogr, 60, 923-925.  
12885656 A.M.Ababneh, C.C.Large, and S.Georghiou (2003).
Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs.
  Biophys J, 85, 1111-1127.  
12824323 M.M.Babu (2003).
NCI: A server to identify non-canonical interactions in protein structures.
  Nucleic Acids Res, 31, 3345-3348.  
12202833 B.Benoff, H.Yang, C.L.Lawson, G.Parkinson, J.Liu, E.Blatter, Y.W.Ebright, H.M.Berman, and R.H.Ebright (2002).
Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.
  Science, 297, 1562-1566.
PDB code: 1lb2
10813836 V.Nanda, and L.Brand (2000).
Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan.
  Proteins, 40, 112-125.  
9547272 F.Cornille, P.Emery, W.Schüler, C.Lenoir, B.Mach, B.P.Roques, and W.Reith (1998).
DNA binding properties of a chemically synthesized DNA binding domain of hRFX1.
  Nucleic Acids Res, 26, 2143-2149.  
9788911 J.Woda, B.Schneider, K.Patel, K.Mistry, and H.M.Berman (1998).
An analysis of the relationship between hydration and protein-DNA interactions.
  Biophys J, 75, 2170-2177.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
9396800 N.M.Luscombe, R.A.Laskowski, and J.M.Thornton (1997).
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
  Nucleic Acids Res, 25, 4940-4945.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
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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