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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLPG, A RHOMBOID FAMILY INTRAMEMBRANE PROTEASE

Authors :   Z. Wu, N. Yan, L. Feng, H. Yan, L. Gu, Y. Shi

Date :   02 Nov 06 (Deposition) - 14 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Integral Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Wu, N. Yan, L. Feng, A. Oberstein, H. Yan, R. P. Baker, L. Gu, P. D. Jeffrey, S. Urban, Y. Shi
Structural Analysis Of A Rhomboid Family Intramembrane Protease Reveals A Gating Mechanism For Substrate Entry.
Nat. Struct. Mol. Biol. V. 13 1084 2006
PubMed-ID: 17099694 | Reference-DOI: 10.1038/NSMB1179
(for further references see the PDB file header)

Molecule 1 - PROTEIN GLPG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	C43 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLPG
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NRF)

(no "Site" information available for 2NRF)

(no "SS Bond" information available for 2NRF)

(no "Cis Peptide Bond" information available for 2NRF)

(no "SAP(SNP)/Variant" information available for 2NRF)

(no "PROSITE Motif" information available for 2NRF)

(no "Exon" information available for 2NRF)

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)
	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:182
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:182
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  
           GLPG_ECOLI    91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA 272
               SCOP domains d2nrfa_ A: GlpG                                                                                                                                                                        SCOP domains
               CATH domains 2nrfA00 A:91-272 Rhomboid-like domains                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nrf A  91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA 272
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:182
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  
           GLPG_ECOLI    91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA 272
               SCOP domains d2nrfb_ B: GlpG                                                                                                                                                                        SCOP domains
               CATH domains 2nrfB00 B:91-272 Rhomboid-like domains                                                                                                                                                 CATH domains
           Pfam domains (1) DUF3582-2-----------------------------Rhomboid-2nrfB03 B:129-272                                                                                                                       Pfam domains (1)
           Pfam domains (2) DUF3582-2-----------------------------Rhomboid-2nrfB04 B:129-272                                                                                                                       Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......---------hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nrf B  91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGW---------NGAHIAGLAVGLAMAFVDSLNA 272
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240|        -|      260       270  
                                                                                                                                                                                241       251

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Rhomboid-like (22)

Superfamily: Rhomboid-like (22)

Family: Rhomboid-like (22)

Protein domain: GlpG (19)

Escherichia coli [TaxId: 562] (19)

1a	d2nrfa_	A:
1b	d2nrfb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Rhomboid-like fold (7)

Homologous Superfamily: Rhomboid-like domains (7)

Escherichia coli. Organism_taxid: 562. (5)

1a	2nrfA00	A:91-272
1b	2nrfB00	B:91-272

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GlnB-like (50)

Family: DUF3582 (6)

Escherichia coli (strain K12) (6)

1a	DUF3582-2nrfB01	B:91-99
1b	DUF3582-2nrfB02	B:91-99

Clan: Rhomboid-like (8)

Family: Rhomboid (8)

Escherichia coli (strain K12) (6)

2a	Rhomboid-2nrfB03	B:129-272
2b	Rhomboid-2nrfB04	B:129-272

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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Description

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