2NR9 - JenaLib

Title :   CRYSTAL STRUCTURE OF GLPG, RHOMBOID PEPTIDASE FROM HAEMOPHILUS INFLUENZAE

Authors :   M. J. Lemieux, S. J. Fischer, M. M. Cherney, K. S. Bateman, M. N. G. James

Date :   01 Nov 06 (Deposition) - 14 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Intramembrane Peptidase, Rhomboid Protease, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Lemieux, S. J. Fischer, M. M. Cherney, K. S. Bateman, M. N. G. James
The Crystal Structure Of The Rhomboid Peptidase From Haemophilus Influenzae Provides Insight Into Intramembrane Proteolysis.
Proc. Natl. Acad. Sci. Usa V. 104 750 2007
PubMed-ID: 17210913 | Reference-DOI: 10.1073/PNAS.0609981104

Compounds

Molecule 1 - PROTEIN GLPG HOMOLOG
	Chains	:	A
	EC Number	:	3.4.21.105
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD-MYCHISA
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLPG
	Mutation	:	YES
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	281310
	Strain	:	86-028NP
	Synonym	:	GLPG, RHOMBOID PEPTIDASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	PA6	3	Ligand/Ion	(R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE
2	PQE	2	Ligand/Ion	3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	PA6	3	Ligand/Ion	(R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE
2	PQE	2	Ligand/Ion	3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	PA6	6	Ligand/Ion	(R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE
2	PQE	4	Ligand/Ion	3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:38 , SER A:55 , PQE A:205	BINDING SITE FOR RESIDUE PA6 A 201
2	AC2	SOFTWARE	TYR A:102 , LYS A:185 , HOH A:264 , HOH A:265	BINDING SITE FOR RESIDUE PA6 A 202
3	AC3	SOFTWARE	MET A:146 , ILE A:182 , LEU A:186 , HOH A:261	BINDING SITE FOR RESIDUE PA6 A 203
4	AC4	SOFTWARE	LYS A:88 , VAL A:103 , PHE A:127 , ILE A:128 , ASN A:166 , SER A:171 , TRP A:179 , ILE A:182 , ASP A:183	BINDING SITE FOR RESIDUE PQE A 204
5	AC5	SOFTWARE	LYS A:10 , LEU A:13 , ILE A:14 , ALA A:17 , LEU A:21 , TRP A:51 , ILE A:54 , SER A:62 , ASN A:63 , ILE A:66 , LEU A:67 , ILE A:75 , GLU A:141 , PA6 A:201	BINDING SITE FOR RESIDUE PQE A 205

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 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)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:192
 aligned with GLPG_HAEIN | P44783 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                                                                                                                                                                                                      192   
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        |-  
           GLPG_HAEIN     4 FLAQQGKITLILTALCVLIYLAQQLGFEDDIMYLMHYPAYEEQDSEVWRYISHTLVHLSNLHILFNLSWFFIFGGMIERTFGSVKLLMLYVVASAITGYVQNYVSGPAFFGLSGVVYAVLGYVFIRDKLNHHLFDLPEGFFTMLLVGIALGFISPLFGVEMGNAAHISGLIVGLIWGFIDSKLRKNSLE---   -
               SCOP domains d2nr9a1 A:4-192 GlpG homolog HI0618                                                                                                                                                          --- SCOP domains
               CATH domains 2nr9A00 A:4-195 Rhomboid-like domains                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------Rhomboid-2nr9A01 A:44-188                                                                                                                        ------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...................hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nr9 A   4 FLAQQGKITLILTALCVLIYIAQQLGFEDDIMYLMHYPAYEEQDSEVWRYISHTLVHLSNLHILFNLSWFFIFGGMIERTFGSVKLLMLYVVASAITGYVQNYVSGPAFFGLSGVVYAVLGYVFIRDKLNHHLFDLPEGFFTMLLVGIALGFISPLFGVEMGNAAHISGLIVGLIWGFIDSKLRKNSLELVP 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193

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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (GLPG_HAEIN | P44783)

molecular function
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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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	Cis Peptide Bonds
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Biological Units
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	2nr9
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