2IRV | pdb_00002irv

Crystal structure of GlpG, a rhomboid intramembrane serine protease

PDB DOI: https://doi.org/10.2210/pdb2IRV/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2006-10-16 Released: 2006-10-31
Deposition Author(s): Bibi, E., Fass, D., Ben-Shem, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.220 (Depositor), 0.236 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for intramembrane proteolysis by rhomboid serine proteases.

Ben-Shem, A., Fass, D., Bibi, E.

(2007) Proc Natl Acad Sci U S A 104: 462-466

PubMed: 17190827 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0609773104
Primary Citation Related Structures:
2IRV

PubMed Abstract:
Intramembrane proteases catalyze peptide bond cleavage of integral membrane protein substrates. This activity is crucial for many biological and pathological processes. Rhomboids are evolutionarily widespread intramembrane serine proteases. Here, we present the 2.3-A-resolution crystal structure of a rhomboid from Escherichia coli. The enzyme has six transmembrane helices, five of which surround a short TM4, which starts deep within the membrane at the catalytic serine residue. Thus, the catalytic serine is in an externally exposed cavity, which provides a hydrophilic environment for proteolysis. Our results reveal a mechanism to enable water-dependent catalysis at the depth of the hydrophobic milieu of the membrane and suggest how substrates gain access to the sequestered rhomboid active site.

Organizational Affiliation

Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. adam.ben-shem@weizmann.ac.il

Macromolecule Content

Total Structure Weight: 48.38 kDa
Atom Count: 3,196
Modeled Residue Count: 355
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein glpG	A, B	182	Escherichia coli K-12	Mutation(s): 0 Gene Names: glpG EC: 3.4.21.105 Membrane Entity: Yes
UniProt
Find proteins for P09391 (Escherichia coli (strain K12)) Explore P09391 Go to UniProtKB: P09391
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09391
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B]	U [auth B], V [auth B], W [auth B], X [auth B]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.220 (Depositor), 0.236 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.82	α = 90
b = 69.35	β = 101.03
c = 67.58	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-10-31

Deposition Author(s):

Bibi, E.

Fass, D.

Ben-Shem, A.

Revision History (Full details and data files)

Version 1.0: 2006-10-31
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Structure summary

2IRV | pdb_00002irv

Crystal structure of GlpG, a rhomboid intramembrane serine protease

Literature

Structural basis for intramembrane proteolysis by rhomboid serine proteases.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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