PROCHECK: a program to check the stereochemical quality of protein structures

Laskowski, Roman A.; MacArthur, Malcolm W.; Moss, David S.; Thornton, Janet M.

doi:10.1107/s0021889892009944

Cited by 22,961 publications

(16,923 citation statements)

References 6 publications

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“…Iterative steps of positional and atomic B-factor refinement followed by manual rebuilding were performed until no further improvement of R factors was achieved. The final model (R work of 20.5% and R free of 24.0%) has good stereochemistry as determined using PROCHEK (34), with all amino acids laying in the most favorable or allowed regions on the Ramachandran plot. No electron density was observed for residues S605-V616, which are assumed to belong to a conformationally flexible loop.…”

Section: Structure Determination and Refinementmentioning

confidence: 94%

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

2004

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Gram-negative bacteria including Escherichia coli, Salmonella typhimurium, and Pseudomonas aeruginosa can modify the structure of lipid A in their outer membrane with 4-amino-4-deoxy-Larabinose (Ara4N). Such modification results in resistance to cationic antimicrobial peptides of the innate immune system and antibiotics such as polymyxin. ArnA is a key enzyme in the lipid A modification pathway, and its deletion abolishes both the Ara4N-lipid A modification and polymyxin resistance. ArnA is a bifunctional enzyme. It can catalyze (i) the NAD + -dependent decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose and (ii) the N-10-formyltetrahydrofolatedependent formylation of UDP-4-amino-4-deoxy-L-arabinose. We show that the NAD + -dependent decarboxylating activity is contained in the 360 amino acid C-terminal domain of ArnA. This domain is separable from the N-terminal fragment, and its activity is identical to that of the full-length enzyme. The crystal structure of the ArnA decarboxylase domain from E. coli is presented here. The structure confirms that the enzyme belongs to the short-chain dehydrogenase/reductase (SDR) family. On the basis of sequence and structure comparisons of the ArnA decarboxylase domain with other members of the short-chain dehydrogenase/reductase (SDR) family, we propose a binding model for NAD + and UDP-glucuronic acid and the involvement of residues T 432 , Y 463 , K 467 ,R 619 , and S 433 in the mechanism of NAD + -dependent oxidation of the 4″-OH of the UDP-glucuronic acid and decarboxylation of the UDP-4-keto-glucuronic acid intermediate.In the process of establishing infections, bacteria must overcome the host defense mechanism including the bactericidal action of cationic antimicrobial peptides (CAMPs). 1 These are small, amphipathic, positively charged peptides that destroy bacteria through membrane permeabilization and constitute a phylogenetically conserved branch of the innate immune system (1-4). In the case of Gram-negative bacteria, CAMPs bind to the bacterial cell surface through electrostatic interactions with the negatively charged groups of the lipopolysaccharide (LPS), the immunogenic glycolipid in the outer membrane in Gram-negative bacteria (5,6). They then traverse to the inner membrane and form a pore, which leads to membrane permeabilization and cell death (7)(8)(9). In addition to their function as a key member of the innate immune system, CAMPs represent an important class of clinical antimicrobials. They have both intrinsic bactericidal activity and appear to enhance the activity of other antibiotics, presumably by facilitating their entry into the microbe (3,10,11 21). The N-terminal domain (residues 1-313) is similar in sequence to other enzymes involved in formyl transfer. However, the relevance of this reaction in the biosynthesis of Ara4N-lipid A is unclear. ArnA is also responsible for the C-4″ oxidation of UDP-GlcA to UDP-4-keto-glucuronic acid and its decarboxylation to yield UDP-4-keto-arabinose (boxed in Figure 1) (20). The C terminus o...

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Section: Structure Determination and Refinementmentioning

confidence: 94%

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

2004

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“…The final model was refined to 3.3 Å with R work =25.9% and R free = 28.2% and contained residues 7-144 and 154-202 from the protein, covering 93% of the protein sequence. The geometry analysis of the final model with Procheck 38 gave statistics of 97.5% and 2.5% for the most favored and additional allowed regions, respectively, on the Ramachandran plot. The pore radius of the ion conduction pathway was analyzed using the program HOLE 39 and the electrostatic potentials were calculated using the program APBS 40 .…”

Section: Methodsmentioning

confidence: 99%

The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture

Lee

Guo

Zeng

et al. 2017

Nature

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TMEM175 is a lysosomal K+ channel important for maintaining the lysosomal membrane potential and pH stability1. It contains two homologous copies of a six-transmembrane (6-TM) domain, which has no sequence homology to the canonical tetrameric K+ channels and lacks the TVGYG selectivity filter motif2–4. Present in a subset of bacteria and archaea, the prokaryotic TMEM175 contains only a single 6-TM domain and functions as a tetramer. Here, we present the crystal structure of a prokaryotic TMEM175 from Chamaesiphon minutus, CmTMEM175, whose architecture represents a completely different fold from that of canonical K+ channels. All six transmembrane helices of CmTMEM175 are tightly packed within each subunit without undergoing domain swap. The highly conserved TM1 acts as the pore lining inner helix, creating an hour-glass shaped ion permeation pathway in the channel tetramer. Three layers of hydrophobic residues on the C-terminal half of TM1s form a bottle neck along the ion conduction pathway and serve as the selectivity filter of the channel. Mutagenesis analysis suggests that the first layer of the highly conserved isoleucine residues in the filter plays the central role in channel selectivity. Thus, the structure of CmTMEM175 represents a novel architecture of a tetrameric cation channel whose ion selectivity mechanism appears distinct from that of the classical K+ channel family.

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“…A homology model of the human AXL tyrosine kinase was constructed utilizing the crystal structure of the IGF-1 receptor kinase domain (PDB: 1JQH) (Pautsch et al, 2001) based on top hits observed when the AXL TK domain was input into PSI-PHI BLAST (NCBI) and 3D-PSSM (Kelley et al, 2000). The model was refined and structural correctness confirmed with PROCHECK (Laskowski et al, 1993). The crystal structure of cMet (PDB: 1ROP) (Schiering et al, 2003) was downloaded and ATP, IM and MP470 were interactively docked utilizing FlexX (Sybyl 7.0, Tripos Inc., St Louis, MO, USA).…”

Section: Homology Modeling and Interactive Dockingmentioning

confidence: 99%

A novel tyrosine kinase switch is a mechanism of imatinib resistance in gastrointestinal stromal tumors

et al. 2007

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KIT or a-platelet-derived growth factor receptor (a-PDGFR) activating mutations are the pathogenic mechanisms that characterize gastrointestinal stromal tumors (GIST). Despite excellent responses to imatinib mesylate (IM), patients are relapsing. We developed an IM-resistant GIST cell line (GIST-R) from the IMsensitive GIST882 cell line (GIST-S) by growing these cells in IM. Gene expression profiling (GEP) of GIST-S, GIST-R cells and two IM resistant GIST patients demonstrated that KIT is downregulated implying a major role in IM resistance. Instead, GIST-R cells have acquired IM resistance by overexpressing the oncogenic receptor tyrosine kinase -AXL -in a 'kinase switch'. Further, the two IM resistant GIST patients express AXL and not c-Kit, seen by immunohistochemistry (IHC). Real time reverse transcriptase-polymerase chain reaction and Western blotting of the GIST-S and GIST-R cells confirmed the switch from Kit to AXL. In GIST-R, AXL is tyrosine phosphorylated and its ligand growtharrest-specific gene 6 is overexpressed implying autocrine activation. The kinase switch is associated with a morphological change from spindle to epithelioid. Molecular modeling of the kinase domain of mutant c-Kit (V654A) and AXL showed no binding to IM but efficient binding to MP470, a novel c-Kit/AXL kinase inhibitor. MP470 synergizes with docetaxel (taxotere) and is cytotoxic to GIST cells.

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PROCHECK: a program to check the stereochemical quality of protein structures

Cited by 22,961 publications

References 6 publications

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture

A novel tyrosine kinase switch is a mechanism of imatinib resistance in gastrointestinal stromal tumors

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PROCHECK: a program to check the stereochemical quality of protein structures

Cited by 22,961 publications

References 6 publications

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance,

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance,

The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture

A novel tyrosine kinase switch is a mechanism of imatinib resistance in gastrointestinal stromal tumors

Contact Info

Product

Resources

About

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,

Crystal Structure ofEscherichia coliArnA (PmrI) Decarboxylase Domain. A Key Enzyme for Lipid A Modification with 4-Amino-4-deoxy-l-arabinose and Polymyxin Resistance^,