Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs).

(2005) Nucleic Acids Res 33

PubMed: 16221976 | PubMedCentral: PMC1253831 | DOI: 10.1093/nar/gki885

Extraction of homologous positions of A domains The ‘Biochemical Algorithms Library’ [BALL, ( 17 )] and a simple Python script were used to extract residues that have at least one atom... at a given distance from the bound phenylalanine in the GrsA-Phe crystal structure [PDB ID 1amu , ( 5 )].

Publication Year: 2005

Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis.

(2009) Nat Chem Biol 5

PubMed: 19182784 | PubMedCentral: PMC2644305 | DOI: 10.1038/nchembio.143

( b ) FAAL28 C-terminal domain of FAAL28 modeled on the basis of PheA (1amu) structure in putative AMP bound conformation (green), acetyl CoA synthetase structure (1pg4) in putative CoA bound conforma... ion (magenta), and FAAL28 N-terminal domain structure (cyan) with highlighted FAAL specific insertion.

Publication Year: 2009

Module evolution and substrate specificity of fungal nonribosomal peptide synthetases involved in siderophore biosynthesis.

(2008) BMC Evol Biol 8

PubMed: 19055762 | PubMedCentral: PMC2644324 | DOI: 10.1186/1471-2148-8-328

A. Ribbon representation of the structure of the activated domain of Gramicidin synthetase (PDB code: 1AMU) bound to its Phe substrate (shown as a CPK model; red) and adenosine monophosphate (AMP; sho... n as " ball & stick " representation of the heavy atoms; light-blue).

Blast searches [ 36 , 37 ] of the Protein Data Bank (PDB) database [ 38 ] , using a subset of A domain sequences from C. heterostrophus NPS2 (AAX09984), F. graminearum NPS2 (FG05372), F. graminearum NPS1 (FG11026), A. nidulans SidC (AN0607), U. maydis sid2 (UM05165), U. maydis fer3 (UM01434), and S. pombe Sib1 (CAB72227) as queries, indicated a high level of similarity with the phenylalanine activating A domain of the NRPS for gramicidin (GrsA), PDB code: 1AMU; [ 25 ].

Using the Combinatorial Extension method [ 39 ] and the 1AMU_A (ie., monomer A of 1AMU) structure as input, other structurally similar proteins with associated crystal structures were identified.

Publication Year: 2008

Algorithm for backrub motions in protein design.

(2008) Bioinformatics 24

PubMed: 18586714 | PubMedCentral: PMC2718647 | DOI: 10.1093/bioinformatics/btn169

The structural model for GrsA-PheA (PDB id: 1amu; Conti et al. , 1997 ) is as described in (Georgiev and Donald, 2007 ).

Publication Year: 2008

Genome scale prediction of substrate specificity for acyl adenylate superfamily of enzymes based on active site residue profiles.

(2010) BMC Bioinformatics 11

PubMed: 20105319 | PubMedCentral: PMC3098103 | DOI: 10.1186/1471-2105-11-57

(a)The crystal structure of adenylation domain of gramicidin synthetase (PDB code: 1AMU ).

Effect of the choice of structural templates on SDRs At the time when the work was carried out, crystal structures were available for adenylation domain of NRPS (PDB code: 1AMU ), luciferases (PDB code: 1LCI ) and acetyl:CoA ligases (PDB code: 1PG4 ).

In method 2, no structural modelling is carried out, instead the crystal structures 1PG3 , 3EQ6 and 1V26 are used, but binding pocket residues are identified based on superposition of the crystal structures on 1AMU .

The position 324 (numbering according to 1AMU ) has a conserved tryptophan in AcCS (substrate C 2 ), whereas in all other subfamilies which utilize larger substrate (>C 2 ), this position has a conserved glycine.

Similarly, in case of 1PG3 , the acetyl CoA ligase, which has a smaller ligand compared to our reference structure phenylalanine bound 1AMU , 8 out of the 15 binding pocket residues were found to be common in the three different methods and the true binding pocket in the acetyl bound structure had only 2 extra residues (Additional file 2 , Table S3).

The structure shown is the adenylation domain of gramicidin synthetase (PDB code: 1AMU ).

The crystal structure of adenylation domain of gramicidin synthetase (PheA) has helped in identification of 10 amino acids forming the substrate (phenylalanine) binding pocket (PDB code: 1AMU ).

However, the SDRs for all subfamilies were identified based on superposition of the modeled structure on 1AMU .

Based on the crystal structure of adenylation domain of gramicidin synthetase (PDB code: 1AMU ) in complex with the substrate phenylalanine, it had been proposed that the substrate selectivity of NRPS adenylation domain is governed by the residues forming the substrate binding pocket [ 32 ].

They are 1PG3 (acetyl CoA ligase), 3EQ6 (medium chain CoA ligase), 1V26 (long chain CoA ligase), 2D1R (luciferase) and 1AMU (adenylation domain of NRPS).

Thus the binding pocket residues identified based on 1AMU agree very well with the true binding pocket as seen in crystal structure and only in case of enzymes having larger substrates additional residues constitute the binding pocket.

Table 4 Results of docking of various substrates onto their cognate enzymes in each subfamily Subfamily % Iden with 1AMU Number of docking runs (GALS) Cluster RMSD (Å) Docking energy Energy Rank Cluster size Population rank Distance (Å) AcCS 18.5 250 1.0 -3.73 4 168 1 3.6 4CL 19.8 250 1.7 -7.74 8 59 2 5.4 MCS 16.3 250 1.7 -8.5 4 6 9 3.1 LCS 18.3 250 1.7 -11.42 3 31 1 4.2 Luciferase 17.7 250 1.7 -11.20 4 61 2 4.3 The table shows the energy and population rank for the cluster having the carboxyl group at interacting distance from the phosphate of AMP.

Since the phenylalanine binding site on 1AMU is in close proximity of the conserved AMP binding site and the catalysis by the superfamily of enzymes involve formation of covalent bond between AMP and acyl group, it was reasonable to assume that other subfamilies will have the acyl group binding site at a position structurally analogous to the Phe binding pocket of 1AMU .

The subdomain A stretches from amino acid 67 to 203 and B subdomain from amino acid 204 to 428 (numbering according to 1AMU ).

In method 1, the sequences were submitted as query to our web server which models long chain:CoA ligases, medium chain CoA ligases and luciferases using the ligand free luciferase structure 1LCI as the template, but identifies binding pocket residues based on superposition of the modeled structure on 1AMU .

We decided to carry out all the docking studies using homology models based on PheA (PDB code: 1AMU ) and compare the results to actual crystal structures wherever available (Additional file 1 , Figure S3).

The sensitivity and specificity are defined as:- Structure analysis For model building, the alignments with the template structure 1AMU were generated by program GenTHREADER [ 57 ].

These include 7 out of the 10 residues which are identified in 1AMU as the substrate binding pocket residues [ 18 ].

The figure depicting the A- (green) and B- (pink) subdomains of the N-terminal domain of 1AMU .

The structure of adenylation domain of gramicidin synthetase (PDB code: 1AMU ) was used as a template and its alignments with the query sequence were obtained from GenTHREADER [ 57 ].

Publication Year: 2010

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity.

(2011) Nucleic Acids Res 39

PubMed: 21558170 | PubMedCentral: PMC3125756 | DOI: 10.1093/nar/gkr323

The structure–function relationship for monomer recruitment by A-domains has been further elucidated by Stachelhaus et al. and Challis et al. by examining the crystal structure of the peptide ... ynthetase gramicidin S synthetase 1 (GrsA, PDB-ID: 1AMU) ( 4–6 ).

We therefore made use of an A-domain crystal structure (PDB-ID: 1AMU) as a template to determine these active site residues.

Signature extraction The set of all active site amino acids, called the signature, was identified by extracting all residues within 8 Å of the substrate phenylalanine in the crystal structure of GrsA (PDB-ID: 1AMU).

Publication Year: 2011

Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models.

(2013) PLoS One 8

PubMed: 23637983 | PubMedCentral: PMC3630128 | DOI: 10.1371/journal.pone.0062136

Similarly, the crystal structure of the phenylalanine-specific A domain [PDB∶1AMU] of gramicidin synthetase A (GrsA) [26] facilitated the identification of 10 residues that line the active sit... pocket of the A domain, and later these were proposed as a sort of substrate specificity conferring code for the A domain [27] , [28] .

Selection of substrate specificity related residues The residues of the aligned AT and A domain sequences were numbered according to the AT domain of E coli FabD [PDB∶1MLA] [24] and the A domain of GrsA [PDB∶1AMU] [26] , respectively.

Publication Year: 2013

Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods.

(2013) PLoS One 8

PubMed: 23874386 | PubMedCentral: PMC3712989 | DOI: 10.1371/journal.pone.0065926

(A) The first nine aminoacids of pdb 1AMU.

It belongs to the Gramicidin Synthetase cluster isolated from Brevibacillus brevis (pdb 1AMU).

The calculation of the spectral moments up to the order k = 3 from the four colours maps is illustrated (downstream figure 6 ) using the first nine amino acids of pdb 1AMU (M 1 V 2 N 3 S 4 S 5 K 6 S 7 I 8 L 9 ).

(C) The final four-color map for pdb 1AMU.

Publication Year: 2013

Adaptation of an L-proline adenylation domain to use 4-propyl-L-proline in the evolution of lincosamide biosynthesis.

(2013) PLoS One 8

PubMed: 24386435 | PubMedCentral: PMC3874040 | DOI: 10.1371/journal.pone.0084902

Homology model construction and structure verification by MD simulation LmbC and CcbC homology models were constructed based on the structure of the phenylalanine specific A-domain of GrsA (called Phe... , PDB ID 1AMU) which has bound AMP and Phe.

Homology model construction The structure of the L-phenylalanine specific A-domain of GrsA (also called PheA, PDB ID 1AMU) was used as a template for the construction of both LmbC and CcbC homology models.

Publication Year: 2013

PubMed ID is not available.

Published in 2007

PubMedCentral: PMC4292098

In addition the AMP binding pockets were ranked according to the similarity of their bound ligand to the AMP ligand of the Protein Data Bank [3] structure 1amu [4].

Publication Year: 2007

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4520716

Molecular replacement (MR) computations were performed in Phaser 44 with the N-terminal body of one monomer of PheA (PDB code 1AMU, residues 17–428) as a search model.

For example, such substitutions are present in the l -phenylalanine-specific PheA (PDB code 1AMU), l -leucine-specific SrfA-C (PDB code 2VQS), and l -valine-specific CytC1 (PDB code 3VNS) NRPS A-domains.

Publication Year: 2014