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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains.

(2005) Nucleic Acids Res 33

PubMed: 16040597 | PubMedCentral: PMC1178005 | DOI: 10.1093/nar/gki709

PDB ids for the displayed structures as follows; 1gcc: GCC-box binding domain; 1bb8: tn916 integrase DNA binding domain; 1kjk: lambda integrase N-terminal domain; 1qqg: Insulin receptor substrate 1 (I... S-1); 1lwt: PI-SceI homing endonuclease DNA binding domain.

Residues involved in contacting DNA in the solution structure of the AP2 domain (pdb id: 1GCC) are shown below the alignment.

Table 1 Most frequent amino acids at DNA-contacting positions (numbered 1–11 and labeled according to 1gcc), according to their order of occurrence, deduced from the solution structure of GCC-box binding domain of ATERF1 (PDB ID 1gcc) and the comprehensive multiple alignment are shown Family 1 R147 2 R150 3 R152 4 W154 5 K156 6 E160 7 R162 8 R170 9 W172 10 T175 11 Y186 ApiAP2 K 27 Y, R, S 24,15,13 D, N 53,14 Q, K, R 18,17,17 R, S, A 23,18,17 Q, E, Y, T 14,10,10,9 Y, K 20,17 K 45 Y, F 52,22 G 88 F, C 28,19 Plant AP2 family R {B} 80 R {G 20} 70 R {G 5,G 20,G 21} 65 W {T 3,A 4} 60 K, R {B} 55, 35 E {C 7} 65 R {G 17,G 18} 65 R {G 8} 75 W {G 5,C 6} 70 T {B} 70 Y {B} 80 Bacterial/Viral AP2 domains K, T, R 27,20,14 S, T, R, Y 27,13,10,10 N, D, H 17,15,15 T, R, S 23,19,13 K, R 44,23 R, Q, T 35,13,13 T, R 21,19 G, K 50,22 F 65 K, L, I 23,19,15 R, A, E 23,19,15 The protein–DNA contacts were identified by using the hydrogen-bond length (3.5 Å) and apolar interaction distance cut-off of 5 Å.

The secondary structure was derived from the solution structure of the AP2 domain (PDB ID: 1GCC).

These conservation patterns were also superimposed onto the NMR structure of the AP2 domain of the Arabidopsis ethylene response TF (ATERF1, PDB: 1GCC) ( 48 ) to understand their structural implications.

The solution structure of the A.thaliana GCC-box binding domain in complex with DNA (PDB Id: 1gcc) is shown.

Publication Year: 2005


Protein-DNA binding specificity predictions with structural models.

(2005) Nucleic Acids Res 33

PubMed: 16246914 | PubMedCentral: PMC1270944 | DOI: 10.1093/nar/gki875

Table 2 Experimental binding site and weight matrix dataset Name PDB code Method (Res., Å) N seq Organism Reference λR 1lmb X-ray (1.8) – a λ-Phage ( 51 ) CroR 6cro X-r... y (3.0) – a λ-Phage ( 52 ) AtERF1 1gcc NMR (NA) – a A.thaliana ( 45 ) c-Myb 1mse NMR (NA) – a M.musculus ( 47 ) Zif268 1aay X-ray (1.6) 6 b M.musculus ( 31 ) Ndt80 1mnn X-ray (1.4) 8 b S.cerevisiae ( 34 ) Gcn4p 1ysa X-ray (2.9) 9 c S.cerevisiae ( 35 , 36 ) MAT a 1/α2 1yrn X-ray (2.5) 19 c S.cerevisiae ( 30 ) EcR/Usp 1r0o X-ray (2.24) 33 c Drosophila melanogaster ( 57 ) Ttk 2drp X-ray (2.8) 16 c D.melanogaster – Prd(homeo) 1fjl X-ray (2.0) 15 c D.melanogaster ( 37 ) Ubx/Exd 1b8i X-ray (2.4) 4 b D.melanogaster – Trl 1yui NMR (NA) 5 c D.melanogaster – MetJ 1mj2 X-ray (2.4) 16 c E.coli ( 32 ) TrpR 1tro X-ray (1.9) 15 c E.coli ( 32 , 33 ) PhoB 1gxp X-ray (2.5) 16 c E.coli ( 32 ) Ihf 1ihf X-ray (2.5) 27 c E.coli ( 32 ) DnaA 1j1v X-ray (2.1) 9 c E.coli ( 32 ) PurR 2puc X-ray (2.7) 23 c E.coli ( 32 ) Crp 1run X-ray (2.7) 50 c E.coli ( 32 ) For protein–DNA structures solved by X-ray crystallography, resolution (Å) is shown in parentheses.

Table 1 Experimental binding affinity dataset Name PDB code Method (Res., Å) ΔΔ G data points Organism Reference Zif268 1aay X-ray (1.6) 15 (8) Mus musculus ( 42 ) Zif268 1aay X-ray (1.6) 6 (6) M.musculus ( 67 ) Zif268 D20A 1jk1 X-ray (1.9) 6 (6) M.musculus ( 67 ) Tus 1ecr X-ray (2.7) 20 (20) Escherichia coli ( 68 ) LacR 1efa X-ray (2.6) 5 (5) E.coli ( 69 ) λR 1lmb X-ray (1.8) 51 (51) λ-Phage ( 51 ) TrpR 1tro X-ray (1.9) 9 (9) E.coli ( 70 ) ER 1hcq X-ray (2.4) 7 (7) Homo sapiens ( 71 ) CroR 6cro X-ray (3.0) 56 (56) λ-Phage ( 52 ) EcoRI 1ckq X-ray (1.85) 13 (13) E.coli ( 41 ) Crp 1run X-ray (2.7) 15 (15) E.coli ( 72 ) BamHI 1bhm X-ray (2.2) 23 (0) Bacillus amyloliquefaciens ( 49 ) PU.1 ETS 1pue X-ray (2.1) 25 (0) M.musculus ( 50 ) Ndt80 1mnn X-ray (1.4) 26 (0) Saccharomyces cerevisiae ( 34 ) MAT a 1/α2 1yrn X-ray (2.5) 54 (0) S.cerevisiae ( 30 ) c-Myb 1mse NMR (NA) 27 (0) M.musculus ( 47 ) AtERF1 1gcc NMR (NA) 21 (0) Arabidopsis thaliana ( 45 ) For protein–DNA structures solved by X-ray crystallography, resolution (Å) is shown in parentheses.

For the dynamic model fit, we additionally exclude all NMR structures (1gcc and 1mse), crystal structures with >2.5 Å resolution (6cro, 2drp, 1run and 2puc) and the Ihf–DNA complex (1ihf) because its DNA conformation cannot be reasonably expected to be modeled by relaxation with the quadratic DNA potential.

Publication Year: 2005


A comparative proteomics resource: proteins of Arabidopsis thaliana.

(2003) Genome Biol 4

PubMed: 12914659 | PubMedCentral: PMC193643 | DOI: 10.1186/gb-2003-4-8-r51

133 complete genomes, 91 partial genomes PAT Sequence homology Function assignment Fold recognition Structure prediction WU-BLAST, PSI-BLAST, 123D, HMMER 103+ genomes, continuous expansion Table 2 Dat... base feature comparison Databases Features Scope Level of integration Learning curve Drawbacks Entrez Genome [ 20 ] Domains from CDD (SMART, PFAM) Proteins by NCBI GI number, accession number, Swiss Prot ID, and so on Structure by PDB ID 3D domains from MMDB Domain relatives by CDART Related sequences using BLINK Visualization using Cn3D Public data All sequences published or voluntarily deposited 1,000+ genomes High Easy to high Complex system Only experimental structural information is available Software interface is not readily available Linkout progress is slow EBI Proteome Analysis Database [ 43 ] InterPro member databases (SwissProt, PFAM, SMART, TIGRFAM, PRINTS, PROSITE, ProDom, PIR SuperFamily) Families, domains and sites by member databases GO annotation Manual curation and integration Precomputed matches against InterPro entries Complete proteomes in SwissProt and TrEMBL 110+ proteomes Medium Easy to moderate SRS based query interface free to academia Basic keyword search possible Sequence based classification MatDB Arabidopsis annotation from PEDANT Free text search Protein categories by structure, function based on SCOP, PIR, InterPro Arabidopsis with limited intergenome comparison Medium Easy to moderate Query response time varies SCOP classification mildly difficult to use Proteins of Arabidopsis thaliana (PAT) database Domains from SCOP, predicted domains from PDP, and full length PDB chains with less than 90% sequence identity (FOLDLIB) GO annotation Precomputed matches against FOLDLIB Template-based structure models Visualization using QuickPDB, Chime Advanced keyword search Hierarchical browsing based on SCOP Related sequences using WU-BLAST Currently 87 Expanding to provide coverage for all known proteomes Medium Easy to Moderate Presentation Style Query flexibility implies a higher learning curve TAIR GO and other ontology development Sequence and map viewer Domains from InterPro Regulatory motif analysis User annotation Comprehensive resource devoted to Arabidopsis Medium Easy to moderate No structural information SUPERFAMILY HMM (SAM) models for SCOP domains Fold recognition Domain architecture visualization 107 genomes Low to medium Easy to moderate Presentation style No update information Gene 3D Structural assignment based on CATH domain classification using PSI-BLAST 66 genomes Low Easy Annotation not dynamically linked to CATH No update information Table 3 Comparison of PAT with other resources (a) Coverage PAT PEDANT/MatDB TAIR/GO EBI Proteomes/InterPro 94% A-E 30.9% PDB 38% ALL 77.3% InterPro 84% A-D 26.7% SCOP 14% Non-IEA 0.07% PDB 65% A-C 46% A-B 38% A (b) Specific examples Target Other sources PAT Results Reliability AP2 domain (1gcc) 140 hits by BLAST against NR 155 hits C (90% certainty) or above 15239082 (At5g11550.1) No hits by PSI-BLAST None from TAIR, PEDANT 1EE4 C 15228210 (At3g47660) FYVE/PHD zinc finger RCC1 like domain Sugar transporter signature (PROSITE) FYVE/PHD zinc finger; RCC1 like domain; PH domain A (99.9% certainty); B (99% certainty); C Cytochrome P450 238 (TAIR GO) 249 hits 256 hits C or above D (50% certainty) or above Protein-kinase-like domain 1037 hits (PEDANT/MatDB) 951 hits (TAIR GO) 1,179 hits C or above Alpha/beta hydrolase fold Arabidopsis 194 hits (PEDANT/MatDB, SCOP 3.65) 340 hits 200 hits C or above A Human 69 hits (PEDANT/MatDB, SCOP c.69) 1,086 hits 1,18 hits C or above A (a) Percent coverage against specific data sources.

The structure of the AP2 domain is found in the PDB (1gcc) [ 21 ].

(b) PDB sequence of 1gcc [ 22 ] was used to perform a standard BLAST search.

Publication Year: 2003


Complementary regulation of four Eucalyptus CBF genes under various cold conditions.

(2009) J Exp Bot 60

PubMed: 19457981 | PubMedCentral: PMC2692017 | DOI: 10.1093/jxb/erp129

The atomic coordinates of the AtERF1-DNA Binding Domain (RCSB Protein Data Bank code 1GCC) ( Allen et al. , 1998 ) were used as a template to build the three-dimensional model of the EguCBF1 AP2-DBD.

Publication Year: 2009


Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)].

(2011) J Exp Bot 62

PubMed: 21414959 | PubMedCentral: PMC3130168 | DOI: 10.1093/jxb/err016

In addition, the secondary structure of this domain as predicted by several secondary structure prediction servers (PHDsec: www.predictprotein.org/; PSIPRED: http://bioinf.cs.ucl.ac.uk/psipred/ ) is q... ite similar to the secondary structure of 1gcc ( Supplementary Fig.

Structure of the DNA-binding domain The structure of the AP2 domain of AtERF1 from Arabidopsis thaliana (PDB code 1gcc) was taken as a template for the comparative modelling of the DNA-binding domain of SiDREB2 ( Fig. 1E ) ( Allen et al. , 1998 ).

Publication Year: 2011


Predicting target DNA sequences of DNA-binding proteins based on unbound structures.

(2012) PLoS One 7

PubMed: 22312425 | PubMedCentral: PMC3270014 | DOI: 10.1371/journal.pone.0030446

PDB Entry name a Protein Seven proteins used as the queries 6CRO RCRO_LAMBD Regulatory protein cro 1MSE MYB_MOUSE Transcriptional activator Myb 1MNN NDT80_YEAST Meiosis-specific transcription factor N... T80 1YRN MATA1_YEAST Mating-type protein A1 1TRO TRPR_ECOLI Trp operon repressor 1RUN CRP_ECOLI Catabolite gene activator 2O61 b NFKB1_HUMAN Nuclear factor NF-kappa-B p105 subunit 13 complexes used for tuning the parameters of the all-atom model 1AAY EGR1_MOUSE Early growth response protein 1 1B8I c UBX_DROME Homeotic protein ultrabithorax EXD_DROME Homeobox protein extradenticle 2DRP TTKB_DROME Protein tramtrack, beta isoform 1FJL PRD_DROME Segmentation protein paired 1GCC ERF1A_ARATH Ethylene-responsive transcription factor 1A 1GXP PHOB_ECOLI Phosphate regulon transcriptional regulatory protein phoB 1J1V DNAA_ECOLI Chromosomal replication initiator protein dnaA 1LMB RPC1_LAMBD Repressor protein CI 1MJ2 METJ_ECOLI Met repressor 2PUC PURR_ECOLI HTH-type transcriptional repressor purR 1R0O USP_DROME Protein ultraspiracle 1YSA GCN4_YEAST General control protein GCN4 1YUI GAGA_DROME Transcription factor GAGA a UniProt entry name.

Publication Year: 2012


Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

(2005) Nucleic Acids Res 33

PubMed: 15673715 | PubMedCentral: PMC548349 | DOI: 10.1093/nar/gki204

Non-TF/DNA refers to 27 non-transcription factor/DNA complexes (including 1mse, 1tro, 1ca5, 2ezd, 1lcc, 1cjg, 1gcc, 1azp, 1az0, 1b69, 1tf3, 1bhm, 1ecr, 1cw0, 1hcr, 1yui, 1sx9, 7icr, 1qaa, 1jey, 1nk2, ... tau, 5gat, 1qrv, 1a73, 2gat and 1j1v), TF/DNA refers to remaining 21 transcription factor complexes (including 1lmb, 1cma, 1apl, 1par, 1run, 1glu, 1nfk, 1efa, 1mdy, 1tsr, 1ipp, 1ytf, 1vkx, 1oct, 1ihf, 1bc7, 1aay, 1cez, 1yrn, 1ysa and 1b3t).

Publication Year: 2005