Exploiting 3D structural templates for detection of metal‐binding sites in protein structures

Goyal, Kshama; Mande, Shekhar C.

doi:10.1002/prot.21601

Cited by 48 publications

(44 citation statements)

References 55 publications

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“…However, upon addition of a mixture of heavy metal ions, RtcB was able to ligate the tRNA halves and circularize the linear intron (lane B), suggesting a requirement for a heavy metal ion. We immediately tried Zn 2þ (lane C-F), as a Zn 2þ -binding site was suggested (12) in the Pyrococcus horikoshii RtcB crystal structure (14). Addition of Zn 2þ successfully substituted for the heavy metal mix (lane C).…”

Section: Resultsmentioning

confidence: 99%

“…Previous analysis of the sequence (17) and structure (12,14) of RtcB suggested a conserved hydrophilic pocket on the surface of the protein (Fig. 4A) might harbor a metal ion binding site, which was predicted to consist of residues Cys98, His203, His234, His404 (12) (Fig. 4 B and C).…”

Section: Rtcb-catalyzed Ligation Incorporates the Phosphate Of The Cymentioning

confidence: 90%

“…A search of the protein structure database revealed that the structure of the P. horikoshii RtcB ortholog was solved as part of a structural genomics project (14). Previous analysis of the sequence (17) and structure (12,14) of RtcB suggested a conserved hydrophilic pocket on the surface of the protein (Fig. 4A) might harbor a metal ion binding site, which was predicted to consist of residues Cys98, His203, His234, His404 (12) (Fig.…”

Section: Rtcb-catalyzed Ligation Incorporates the Phosphate Of The Cymentioning

confidence: 98%

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Archaeal 3′-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation

Englert

Sheppard

Aslanian

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

106

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Intron removal from tRNA precursors involves cleavage by a tRNA splicing endonuclease to yield tRNA 3′-halves beginning with a 5′-hydroxyl, and 5′-halves ending in a 2′,3′-cyclic phosphate. A tRNA ligase then incorporates this phosphate into the internucleotide bond that joins the two halves. Although this 3′-P RNA splicing ligase activity was detected almost three decades ago in extracts from animal and later archaeal cells, the protein responsible was not yet identified. Here we report the purification of this ligase from Methanopyrus kandleri cells, and its assignment to the still uncharacterized RtcB protein family. Studies with recombinant Pyrobaculum aerophilum RtcB showed that the enzyme is able to join spliced tRNA halves to mature-sized tRNAs where the joining phosphodiester linkage contains the phosphate originally present in the 2′,3′-cyclic phosphate. The data confirm RtcB as the archaeal RNA 3′-P ligase. Structural genomics efforts previously yielded a crystal structure of the Pyrococcus horikoshii RtcB protein containing a new protein fold and a conserved putative Zn 2þ binding cleft. This structure guided our mutational analysis of the P. aerophilum enzyme. Mutations of highly conserved residues in the cleft (C100A, H205A, H236A) rendered the enzyme inactive suggesting these residues to be part of the active site of the P. aerophilum ligase. There is no significant sequence similarity between the active sites of P. aerophilum ligase and that of T4 RNA ligase, nor ligases from plants and fungi. RtcB sequence conservation in archaea and in eukaryotes implicates eukaryotic RtcB as the long-sought animal 3′-P RNA ligase.ligation | tRNA biosynthesis | RNA processing E ukaryotes and archaea contain a number of intron-containing tRNA genes. After their transcription the intron is cleaved from the precursor tRNA by the splicing endonuclease. The resulting tRNA halves are then joined by a tRNA ligase to form mature-sized tRNA (1). The cleavage by the tRNA splicing endonuclease leaves the 5′ exon with a 2′,3′-cyclic phosphate terminus and the 3′ exon with a 5′-hydroxyl group (2). The wellknown multifunctional yeast tRNA ligase, a class I 5′-P RNA ligase (RNL) (3), is unable to directly join these ends together (4). Instead, the class I 5′-P RNL uses its 2′,3′-cyclic-3′-phophodiesterase and 5′-RNA polynucleotide kinase activities to yield a 2′-phosphate-3′-hydroxyl and a 5′-phosphate, which the yeast enzyme then joins via formation of a 2′-phosphate-3′,5′-phosphodiester bond in an ATP-dependent reaction. In plants, mature tRNAs are formed in a similar manner by the class II 5′-P RNL (5, 6).Although the 5′-P ligation pathway is known to exist in animals, almost 30 years ago a different RNA ligase activity was discovered in HeLa cell extracts (7). This 3′-P RNL ligates tRNA 3′-halves beginning with a 5′-hydroxyl, and 5′-halves ending in a 2′,3′-cyclic phosphate by incorporating this phosphate into the internucleotide bond that joins the two halves. Attempts to purify this activity to homogeneity were unsuccess...

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Section: Resultsmentioning

confidence: 99%

Section: Rtcb-catalyzed Ligation Incorporates the Phosphate Of The Cymentioning

confidence: 90%

Section: Rtcb-catalyzed Ligation Incorporates the Phosphate Of The Cymentioning

confidence: 98%

See 1 more Smart Citation

Archaeal 3′-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation

Englert

Sheppard

Aslanian

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

106

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“…3C). The CEN2 NMR structure was docked to the MyTH4 domain using the program HADDOCK (21). The final docked structure reveals a good surface match between CEN2 and MyTH4, and the CEN2 peptide fits reasonably well with the unexplained electron densities observed in MyTH4 (Fig.…”

mentioning

confidence: 89%

HSPC117 Is the Essential Subunit of a Human tRNA Splicing Ligase Complex

Popow

Englert

Weitzer

et al. 2011

Science

219

300

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“…There have been several prediction methods based on structural information, such as the threading model (Sodhi et al 2004;Goyal et al 2008) and the force field model (Schymkowitz et al 2005). An empirical method based on the comparison of holo-apo pairs of known metal-binding sites appears to be one of the most practical approaches currently available because of the quality of the results (Babor et al 2008).…”

Section: Search By Amino Acid Sequencementioning

confidence: 99%

MetalMine: a database of functional metal-binding sites in proteins

Nakamura¹,

Hirai²,

Altaf‐Ul‐Amin³

et al. 2009

Plant Biotechnology

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We present a new database called MetalMine that contains the classification of metal-binding sites derived from the structures of protein-metal-ion complexes. Metal-binding sites were automatically extracted from Protein Data Bank (PDB) structures, classified based on the protein domains in which the metal-binding sites are incorporated, and then manually curated. Tentative or artificial metal ion coordinations were excluded during this curation process. On the web pages of the database, the following information about metal-binding sites is presented in a hierarchical manner: the kind of metal ion, metal-binding site typically specified by the name of the protein, and each instance of metal-binding coordinates in the PDB structures. The database search engine currently supports the following two types of queries. First, given the PDB code of a protein-metal-ion complex, it provides a list of metal-binding sites incorporated in the structure file. Second, given an amino acid sequence as a query, it looks for matches with metal-binding residues in the Basic Local Alignment Search Tool (BLAST) sequence alignment. As of October 2009, MetalMine contained 412 classified entries of functional metal-binding sites, which we believe is the largest number of entries in databases available to the public.

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Exploiting 3D structural templates for detection of metal‐binding sites in protein structures

Cited by 48 publications

References 55 publications

Archaeal 3′-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation

Archaeal 3′-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation

HSPC117 Is the Essential Subunit of a Human tRNA Splicing Ligase Complex

MetalMine: a database of functional metal-binding sites in proteins

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