4V0H | pdb_00004v0h

Human metallo beta lactamase domain containing protein 1 (hMBLAC1)

PDB DOI: https://doi.org/10.2210/pdb4V0H/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-16 Released: 2016-01-13
Deposition Author(s): Pettinati, I., McDonough, M.A., Brem, J., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.193 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease.

Pettinati, I., Grzechnik, P., Ribeiro de Almeida, C., Brem, J., McDonough, M.A., Dhir, S., Proudfoot, N.J., Schofield, C.J.

(2018) Elife 7

PubMed: 30507380 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.39865
Primary Citation Related Structures:
4V0H

PubMed Abstract:
Replication-dependent (RD) core histone mRNA produced during S-phase is the only known metazoan protein-coding mRNA presenting a 3' stem-loop instead of the otherwise universal polyA tail. A metallo β-lactamase (MBL) fold enzyme, cleavage and polyadenylation specificity factor 73 (CPSF73), is proposed to be the sole endonuclease responsible for 3' end processing of both mRNA classes. We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle. Depletion of MBLAC1 in cells significantly affects cell cycle progression thus identifying MBLAC1 as a new type of S-phase-specific cancer target.

Organizational Affiliation

Department of Chemistry, University of Oxford, Oxford, United Kingdom.

Macromolecule Content

Total Structure Weight: 109.64 kDa
Atom Count: 6,787
Modeled Residue Count: 885
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METALLO-BETA-LACTAMASE DOMAIN-CONTAINING PROTEIN 1 1	A, B, C, D	266	Homo sapiens	Mutation(s): 0 EC: 3 (PDB Primary Data), 3.1.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for A4D2B0 (Homo sapiens) Explore A4D2B0 Go to UniProtKB: A4D2B0
PHAROS: A4D2B0 GTEx: ENSG00000214309
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4D2B0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	I [auth B], L [auth C], O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] J [auth C] E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.211 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.193 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.95	α = 109.31
b = 67.13	β = 105.4
c = 67.9	γ = 90.17

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2018-02-21
Changes: Database references
Version 1.2: 2019-11-20
Changes: Database references, Other
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations