PDBsum entry 1r5c

Hydrolase

PDB id: 1r5c

Contents

Protein chains

124 a.a. *

Ligands

CPA ×2

Waters ×91

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.

Authors

A.Merlino, L.Vitagliano, F.Sica, A.Zagari, L.Mazzarella.

Ref.

Biopolymers, 2004, 73, 689-695.

PubMed id

15048772

Abstract

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.

Secondary reference #1

Title

Bovine seminal ribonuclease: structure at 1.9 a resolution.

Authors

L.Mazzarella, S.Capasso, D.Demasi, G.Di lorenzo, C.A.Mattia, A.Zagari.

Ref.

Acta Crystallogr D Biol Crystallogr, 1993, 49, 389-402. [DOI no: 10.1107/S0907444993003403]

PubMed id

15299514

Figure 13.
Fig. 13. Histogram showing the distribution of the thermal factors for water molecules.

Figure 14.
Fig. 14. A group of highly conserved water molecules for S1. Broken lines indicate hydrogen bonds involving water molecules. The same pattern is also observed for $2 and for RNase A.

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #2

Title

Binding of a substrate analog to a domain swapping protein: X-Ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')Adenosine.

Authors

L.Vitagliano, S.Adinolfi, A.Riccio, F.Sica, A.Zagari, L.Mazzarella.

Ref.

Protein Sci, 1998, 7, 1691-1699. [DOI no: 10.1002/pro.5560070804]

PubMed id

10082366

Figure 2.
Fig. 2. - 2Fc omitmapsoftheregion 16-22. (A) Subunit SA showingthe two alternativeconformationsofthe HP and B) subunit SB. The mapswerecontoured at la. Figure continues n next page.)

Figure 3.
Fig. 3. o - , omit map contoured at u of thebounddinucleotide n one of the two active ites. heelectrondensity for hesecond ite is equallywelldefined.

The above figures are reproduced from the cited reference with permission from the Protein Society

Secondary reference #3

Title

Cosolute effect on crystallization of two dinucleotide complexes of bovine seminal ribonuclease from concentrated salt solutions

Authors

F.Sica, S.Adinolfi, L.Vitagliano, A.Zagari, S.Capasso, L.Mazzarella.

Ref.

j cryst growth, 1996, 168, 192.

Secondary reference #4

Title

A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.

Authors

L.Vitagliano, S.Adinolfi, F.Sica, A.Merlino, A.Zagari, L.Mazzarella.

Ref.

J Mol Biol, 1999, 293, 569-577. [DOI no: 10.1006/jmbi.1999.3158]

PubMed id

10543951

Figure 1.
Figure 1. Omit electron density map calculated with Fourier coefficients Fo - Fc of the dinucleotide bound at one active site contoured to 2.2s. This picture was generated using the program O (Jones et al., 1991).

Figure 6.
Figure 6. Space-filling representation of the dimer and the substrate analogue bound at the interface site.

The above figures are reproduced from the cited reference with permission from Elsevier