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Title :   A COMPLEX OF GLPG WITH ISOCOUMARIN INHIBITOR COVALENTLY BONDED TO SERINE 201 AND HISTIDINE 150

Authors :   K. R. Vinothkumar, O. Voskya, E. V. Wolf, A. J. Brouwer, R. M. J. Liskamp, S. H. L. Verhelst

Date :   04 Dec 12 (Deposition) - 13 Feb 13 (Release) - 06 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Intra-Membrane Protease, Serine Protease, Acyl Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Vosyka, K. R. Vinothkumar, E. V. Wolf, A. J. Brouwer, R. M. J. Liskamp S. H. L. Verhelst
Activity-Based Probes For Rhomboid Proteases Discovered In A Mass Spectrometry-Based Assay.
Proc. Natl. Acad. Sci. Usa V. 110 2472 2013
PubMed-ID: 23359682 | Reference-DOI: 10.1073/PNAS.1215076110

Compounds

Molecule 1 - RHOMBOID PROTEASE GLPG
	Chains	:	A
	EC Number	:	3.4.21.105
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	C41
	Expression System Vector	:	PET
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE TM DOMAIN, RESIDUES 92-270
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Other Details	:	THE ISOCOUMARIN RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 FORMS ESTER BOND AND SUBSEQUENTLY A REACTION BETWEEN HISTIDINE CREATES A SECOND COVALENT BOND.
	Synonym	:	INTRAMEMBRANE SERINE PROTEASE, GLPG

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:146 , HIS A:150 , HOH A:2010	BINDING SITE FOR RESIDUE CL A 402
2	AC2	SOFTWARE	ILE A:175	BINDING SITE FOR RESIDUE BNG A 403
3	AC3	SOFTWARE	PHE A:139	BINDING SITE FOR RESIDUE BNG A 405
4	AC4	SOFTWARE	TRP A:122 , PHE A:127 , ASP A:128 , LEU A:131	BINDING SITE FOR RESIDUE BNG A 406
5	AC5	SOFTWARE	LEU A:156 , TRP A:157	BINDING SITE FOR RESIDUE BNG A 407
6	AC6	SOFTWARE	MET A:149 , HIS A:150 , PHE A:153 , ASN A:154 , SER A:201 , TYR A:205 , TRP A:236 , GLY A:240 , PHE A:245 , MET A:249 , HOH A:2010	BINDING SITE FOR LIGAND SV1 A 401 BOUND TO SER A 201 AND HIS A 150

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:179
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:179
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
           GLPG_ECOLI    92 RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSL 270
               SCOP domains d3zeba_ A: GlpG                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zeb A  92 RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSL 270
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GLPG_ECOLI | P09391)

molecular function
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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