1yt3 Summary

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Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

The structure was published by Zuo, Y., Wang, Y., and Malhotra, A., in 2005 in a paper entitled "Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.6 Å and deposited in 2005.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of Ribonuclease D. This molecule has the UniProt identifier P09155 (RND_ECOLI)search. The sample contained 375 residues which is 100% of the natural sequence. Out of 375 residues 375 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Ribonuclease D P09155 (1-375) (RND_ECOLI)search Escherichia coli K-12search 100% 375 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P09155 (1 - 375) Ribonuclease D Escherichia coli

Chain Structural classification (SCOP) Sequence family (Pfam)
A (P09155) RNase D C-terminal domainssearch, DnaQ-like 3'-5' exonucleasesearch PF00570: HRDC domainsearch, PF01612: 3'-5' exonucleasesearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A (P09155) 3'-5' exonuclease activitysearch catalytic activitysearch nucleic acid bindingsearch nucleotide bindingsearch ribonuclease D activitysearch exonuclease activitysearch hydrolase activitysearch ribonuclease activitysearch nuclease activitysearch cellular metabolic processsearch tRNA processingsearch RNA phosphodiester bond hydrolysis, exonucleolyticsearch nucleobase-containing compound metabolic processsearch nucleic acid phosphodiester bond hydrolysissearch tRNA 3'-end processingsearch RNA phosphodiester bond hydrolysissearch intracellularsearch cytoplasmsearch

Chain InterPro annotation
A HRDC domainsearch 3'-5' exonuclease domainsearch Ribonuclease Dsearch HRDC-likesearch Ribonuclease H-like domainsearch