2XTV - JenaLib

Title :   STRUCTURE OF E.COLI RHOMBOID PROTEASE GLPG, ACTIVE SITE MUTANT, S201T, ORTHORHOMBIC CRYSTAL FORM

Authors :   K. R. Vinothkumar

Date :   12 Oct 10 (Deposition) - 02 Feb 11 (Release) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

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

Reference :   K. R. Vinothkumar
Structure Of Rhomboid Protease In A Lipid Environment
J. Mol. Biol. V. 407 232 2011
PubMed-ID: 21256137 | Reference-DOI: 10.1016/J.JMB.2011.01.029

Compounds

Molecule 1 - RHOMBOID PROTEASE GLPG
	Chains	:	A
	EC Number	:	3.4.21.105
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	C41
	Expression System Vector Type	:	PLASMID
	Fragment	:	CORE TM DOMAIN, RESIDUES 93-272
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Synonym	:	INTRAMEMBRANE SERINE PROTEASE, GLPG

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:130 , PHE A:133 , GLU A:134 , PHE A:135 , TRP A:136 , ARG A:217 , ALA A:263 , PHE A:266 , MC3 A:503 , MC3 A:505 , HOH A:2076	BINDING SITE FOR RESIDUE MC3 A 501
02	AC2	SOFTWARE	TRP A:122 , PHE A:153 , LEU A:156 , TRP A:157 , TRP A:159 , TYR A:160 , GLN A:226 , PHE A:232 , PHE A:245 , HOH A:2077	BINDING SITE FOR RESIDUE MC3 A 502
03	AC3	SOFTWARE	TRP A:136 , PHE A:153 , LEU A:155 , LEU A:156 , TRP A:159 , PHE A:266 , LEU A:270 , MC3 A:501 , MC3 A:509 , MC3 A:511 , HOH A:2079	BINDING SITE FOR RESIDUE MC3 A 503
04	AC4	SOFTWARE	LEU A:184 , ALA A:256 , ALA A:263 , MC3 A:512	BINDING SITE FOR RESIDUE MC3 A 504
05	AC5	SOFTWARE	LYS A:132 , TYR A:138 , TRP A:212 , GLU A:216 , MC3 A:501 , MC3 A:506 , MC3 A:507 , MC3 A:508	BINDING SITE FOR RESIDUE MC3 A 505
06	AC6	SOFTWARE	VAL A:106 , ILE A:109 , LEU A:234 , MC3 A:505 , MC3 A:508 , MC3 A:512	BINDING SITE FOR RESIDUE MC3 A 506
07	AC7	SOFTWARE	TRP A:125 , LEU A:183 , GLN A:190 , MC3 A:505 , MC3 A:508	BINDING SITE FOR RESIDUE MC3 A 507
08	AC8	SOFTWARE	TYR A:187 , MC3 A:505 , MC3 A:506 , MC3 A:507	BINDING SITE FOR RESIDUE MC3 A 508
09	AC9	SOFTWARE	PHE A:139 , ILE A:175 , LEU A:179 , MC3 A:503 , MC3 A:510	BINDING SITE FOR RESIDUE MC3 A 509
10	BC1	SOFTWARE	MC3 A:509	BINDING SITE FOR RESIDUE MC3 A 510
11	BC2	SOFTWARE	GLN A:112 , MC3 A:503 , MC3 A:512	BINDING SITE FOR RESIDUE MC3 A 511
12	BC3	SOFTWARE	TYR A:187 , MC3 A:504 , MC3 A:506 , MC3 A:511	BINDING SITE FOR RESIDUE MC3 A 512
13	BC4	SOFTWARE	PHE A:242 , VAL A:267 , ASN A:271	BINDING SITE FOR RESIDUE MC3 A 513
14	BC5	SOFTWARE	ILE A:102 , PHE A:242 , ASP A:243	BINDING SITE FOR RESIDUE MC3 A 514

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

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Chain A from PDB  Type:PROTEIN  Length:178
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:180
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
           GLPG_ECOLI    93 AGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA 272
               SCOP domains d2xtva_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains DUF3582-----------------------------Rhomboid-2xtvA02 A:129-272                                                                                                                       Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...--..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xtv A  93 AGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLTGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLF--SMANGAHIAGLAVGLAMAFVDSLNA 272
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |  | 252       262       272
                                                                                                                                                                                  245  |                        
                                                                                                                                                                                     248

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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 (0, 0)

Pfam Domains (2, 2)

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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