3B45 - JenaLib

Title :   CRYSTAL STRUCTURE OF GLPG AT 1.9A RESOLUTION

Authors :   Y. Wang, S. Maegawa, Y. Akiyama, Y. Ha

Date :   23 Oct 07 (Deposition) - 22 Jan 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Intramembrane Protease, Integral Membrane Protein, Serine Protease, Dna-Binding, Glycerol Metabolism, Inner Membrane, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wang, S. Maegawa, Y. Akiyama, Y. Ha
The Role Of L1 Loop In The Mechanism Of Rhomboid Intramembrane Protease Glpg.
J. Mol. Biol. V. 374 1104 2007
PubMed-ID: 17976648 | Reference-DOI: 10.1016/J.JMB.2007.10.014
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 17)

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:91 , ARG A:92 , ALA A:93 , TRP A:159 , GLY A:163 , BNG A:502 , HOH A:527 , HOH A:573 , HOH A:574 , HOH A:584 , HOH A:591	BINDING SITE FOR RESIDUE BNG A 501
02	AC2	SOFTWARE	TYR A:160 , GLN A:226 , BNG A:501 , HOH A:573 , HOH A:574 , HOH A:584	BINDING SITE FOR RESIDUE BNG A 502
03	AC3	SOFTWARE	VAL A:99 , BNG A:515	BINDING SITE FOR RESIDUE BNG A 503
04	AC4	SOFTWARE	VAL A:96 , PHE A:135 , BNG A:512 , BNG A:515	BINDING SITE FOR RESIDUE BNG A 504
05	AC5	SOFTWARE	MET A:100 , PHE A:139 , BNG A:515	BINDING SITE FOR RESIDUE BNG A 505
06	AC6	SOFTWARE	PHE A:153 , PHE A:232	BINDING SITE FOR RESIDUE BNG A 506
07	AC7	SOFTWARE	ALA A:250 , GLY A:252 , ALA A:253 , ILE A:255 , BNG A:510 , HOH A:561 , HOH A:565	BINDING SITE FOR RESIDUE BNG A 507
08	AC8	SOFTWARE	VAL A:238 , TRP A:241	BINDING SITE FOR RESIDUE BNG A 508
09	AC9	SOFTWARE	TRP A:98 , ILE A:102 , MET A:208 , GLY A:209 , TRP A:212 , GLU A:216	BINDING SITE FOR RESIDUE BNG A 509
10	BC1	SOFTWARE	VAL A:267 , LEU A:270 , BNG A:507	BINDING SITE FOR RESIDUE BNG A 510
11	BC2	SOFTWARE	TRP A:122 , ASP A:128	BINDING SITE FOR RESIDUE BNG A 511
12	BC3	SOFTWARE	PHE A:133 , BNG A:504	BINDING SITE FOR RESIDUE BNG A 512
13	BC4	SOFTWARE	ALA A:110	BINDING SITE FOR RESIDUE BNG A 513
14	BC5	SOFTWARE	PHE A:135 , BNG A:503 , BNG A:504 , BNG A:505	BINDING SITE FOR RESIDUE BNG A 515
15	BC6	SOFTWARE	TRP A:241	BINDING SITE FOR RESIDUE BNG A 516

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:180
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:180
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
           GLPG_ECOLI    91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSL 270
               SCOP domains d3b45a_ A: GlpG                                                                                                                                                                      SCOP domains
               CATH domains 3b45A00 A:91-270 Rhomboid-like 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
                 3b45 A  91 ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSL 270
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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	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 (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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