PDBsum entry 1vcz

Hydrolase

PDB id

1vcz

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Contents

			Protein chain

					204 a.a. *

			Ligands

					5GP ×2

			Waters ×92

* Residue conservation analysis

PDB id:

1vcz

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Name:

Hydrolase

Title:

Crystal structure of the rnase nt in complex with 5'-gmp

Structure:

Rnase ngr3. Chain: a. Synonym: ribonuclease nt, rnase nt. Engineered: yes

Source:

Nicotiana glutinosa. Organism_taxid: 35889. Tissue: leaves. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

1.80Å

R-factor:

0.217

R-free:

0.252

Authors:

S.Kawano,Y.Kakuta,M.Kimura

Key ref:

S.Kawano et al. (2006). Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex with nucleoside monophosphates. J Biochem (tokyo), 140, 375-381. PubMed id: 16870673

Date:

17-Mar-04

Release date:

26-Apr-05

PROCHECK

	Headers

	References

Protein chain

Q9SSV1 (Q9SSV1_NICGU) - RNase NGR3 from Nicotiana glutinosa

Seq: Struc:					236 a.a. 204 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.1.27.1 - Transferred entry: 4.6.1.19.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.

	J Biochem (tokyo) 140:375-381 (2006)
PubMed id: 16870673

Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex with nucleoside monophosphates.
S.Kawano, Y.Kakuta, T.Nakashima, M.Kimura.

ABSTRACT

Ribonuclease NT (RNase NT), induced upon tobacco mosaic virus (TMV) infection in Nicotiana glutinosa leaves, has a broad base specificity. The crystal structures of RNase NT in complex with either 5'-AMP, 5'-GMP, or 2'-UMP were determined at 1.8 A resolutions by molecular replacement. RNase NT consists of seven helices and seven beta strands, and the structure is highly similar to that of RNase NW, a guanylic acid preferential RNase from the N. glutinosa leaves, showing root mean square deviation (rmsd) of 1.1 A over an entire length of two molecules for Calpha atoms. The complex structures revealed that Trp42, Asn44, and Trp50 are involved in interactions with bases at B1 site (primary site), whereas Gln12, Tyr17, Ser78, Leu79, and Phe89 participate in recognition of bases at B2 site (subsite). The 5'-GMP and 5'-AMP bind both B1 and B2 sites in RNase NT, while 2'-UMP predominantly binds B1 site in the complex. The nucleotide binding modes in these complexes would provide a clue to elucidation of structural basis for the broad base specificity for RNase NT.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20843477

E.F.Fang, and T.B.Ng (2011).
Ribonucleases of different origins with a wide spectrum of medicinal applications.

Biochim Biophys Acta, 1815, 65-74.

20854710

W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.

Q Rev Biophys, 44, 1.

20189811

N.Luhtala, and R.Parker (2010).
T2 Family ribonucleases: ancient enzymes with diverse roles.

Trends Biochem Sci, 35, 253-259.

18305191

S.M.Rodriguez, S.Panjikar, K.Van Belle, L.Wyns, J.Messens, and R.Loris (2008).
Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.

Protein Sci, 17, 681-690.

PDB code:

2z70

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.