3PQV | pdb_00003pqv

Cyclase homolog

PDB DOI: https://doi.org/10.2210/pdb3PQV/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Kluyveromyces lactis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-27 Released: 2011-04-13
Deposition Author(s): Tanaka, N., Smith, P., Shuman, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.259 (Depositor), 0.253 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Rcl1, an essential component of the eukaryal pre-rRNA processosome implicated in 18s rRNA biogenesis.

Tanaka, N., Smith, P., Shuman, S.

(2011) RNA 17: 595-602

PubMed: 21367972 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1261/rna.2571811
Primary Citation Related Structures:
3PQV

PubMed Abstract:
Rcl1 is an essential nucleolar protein required for U3 snoRNA-guided pre-rRNA processing at sites flanking the 18S rRNA sequence. A potential catalytic role for Rcl1 during pre-rRNA cleavage has been suggested based on its primary structure similarity to RNA 3'-terminal phosphate cyclase (Rtc) enzymes, which perform nucleotidyl transfer and phosphoryl transfer reactions at RNA ends. Here, we report the 2.6 Å crystal structure of a biologically active yeast Rcl1, which illuminates its modular 4-domain architecture and overall homology with RNA cyclases while revealing numerous local differences that account for why Rtcs possess metal-dependent adenylyltransferase activity and Rcls do not. A conserved oxyanion-binding site in Rcl1 was highlighted for possible catalytic or RNA-binding functions. However, the benign effects of mutations in and around the anion site on Rcl1 activity in vivo militate against such a role.

Organizational Affiliation

Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA.

Macromolecule Content

Total Structure Weight: 161.45 kDa
Atom Count: 11,342
Modeled Residue Count: 1,409
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rcl1 protein	A, B, C, D	365	Kluyveromyces lactis	Mutation(s): 0 Gene Names: KLLA0C05984g
UniProt
Find proteins for Q6CUC5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CUC5 Go to UniProtKB: Q6CUC5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6CUC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], J [auth D], K [auth D]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.259 (Depositor), 0.253 (DCC)
R-Value Work: 0.204 (Depositor), 0.200 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.317	α = 90
b = 138.821	β = 90
c = 228.945	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Tanaka, N.

Smith, P.

Shuman, S.

Revision History (Full details and data files)

Version 1.0: 2011-04-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations