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(-) Description

Title :  CRYSTAL STRUCTURE OF GLPG, A RHOMBOID INTRAMEMBRANE SERINE PROTEASE
 
Authors :  E. Bibi, D. Fass, A. Ben-Shem
Date :  16 Oct 06  (Deposition) - 31 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane Protein, Cavity, Ser-His Dyad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ben-Shem, D. Fass, E. Bibi
Structural Basis For Intramembrane Proteolysis By Rhomboid Serine Proteases.
Proc. Natl. Acad. Sci. Usa V. 104 462 2007
PubMed-ID: 17190827  |  Reference-DOI: 10.1073/PNAS.0609773104

(-) Compounds

Molecule 1 - PROTEIN GLPG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTEASE CORE, RESIDUES 92-273
    Gene: GLPG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1LDA16Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
2LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
3PGV4Ligand/Ion(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1LDA3Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
2LMT-1Ligand/IonDODECYL-BETA-D-MALTOSIDE
3PGV-1Ligand/Ion(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (4, 19)
No.NameCountTypeFull Name
1LDA13Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
2LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
3PGV4Ligand/Ion(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:14 , TRP B:212 , ARG B:227 , GLY B:228 , ILE B:230 , LDA B:3847BINDING SITE FOR RESIDUE PO4 B 5156
02AC2SOFTWARELDA A:3842 , HOH B:69 , VAL B:106 , ILE B:113 , LEU B:114BINDING SITE FOR RESIDUE LDA B 3834
03AC3SOFTWAREVAL A:106 , TRP B:98 , ILE B:102 , LDA B:3836BINDING SITE FOR RESIDUE LDA B 3835
04AC4SOFTWARELDA A:3845 , PRO B:95 , ILE B:102 , LDA B:3835BINDING SITE FOR RESIDUE LDA B 3836
05AC5SOFTWAREMET B:101 , PHE B:108 , LEU B:148 , LEU B:155 , LEU B:156 , TRP B:159BINDING SITE FOR RESIDUE LDA B 3837
06AC6SOFTWAREVAL B:96 , SER B:171BINDING SITE FOR RESIDUE LDA B 3838
07AC7SOFTWARELDA A:3845BINDING SITE FOR RESIDUE LDA B 3839
08AC8SOFTWARETRP B:241 , LMT B:3888BINDING SITE FOR RESIDUE LDA B 3840
09AC9SOFTWAREHOH B:61 , TRP B:241 , PHE B:242BINDING SITE FOR RESIDUE LDA B 3841
10BC1SOFTWAREGLY A:94 , PRO A:95 , TRP A:98 , VAL A:99 , LDA B:3834BINDING SITE FOR RESIDUE LDA A 3842
11BC2SOFTWARELDA B:3844BINDING SITE FOR RESIDUE LDA B 3843
12BC3SOFTWARELDA B:3843BINDING SITE FOR RESIDUE LDA B 3844
13BC4SOFTWARELDA B:3836 , LDA B:3839BINDING SITE FOR RESIDUE LDA A 3845
14BC5SOFTWAREPHE A:242 , TRP B:212 , ILE B:230 , ILE B:231 , PO4 B:5156BINDING SITE FOR RESIDUE LDA B 3847
15BC6SOFTWARETRP A:159 , TYR A:160BINDING SITE FOR RESIDUE LDA A 3850
16BC7SOFTWAREHOH B:32 , HOH B:47 , HOH B:63 , LEU B:184 , PHE B:192 , SER B:193 , SER B:248 , MET B:249 , GLY B:252 , ALA B:256 , LDA B:3840BINDING SITE FOR RESIDUE LMT B 3888
17BC8SOFTWAREHOH B:18 , HOH B:78 , HIS B:150 , PHE B:153 , ASN B:154 , TRP B:157 , SER B:201 , TYR B:205 , PHE B:232 , TRP B:236 , HIS B:254BINDING SITE FOR RESIDUE PGV B 5136
18BC9SOFTWARELEU B:229 , PHE B:232BINDING SITE FOR RESIDUE PGV B 5138
19CC1SOFTWARETRP B:236BINDING SITE FOR RESIDUE PGV B 5139

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IRV)

(-) 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:176
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:182
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           GLPG_ECOLI    92 RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNAR 273
               SCOP domains d2irva_ A: GlpG                                                                                                                                                                        SCOP domains
               CATH domains 2irvA00 A:92-273 Rhomboid-like domains                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..------..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2irv A  92 RAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFD------ANGAHIAGLAVGLAMAFVDSLNAR 273
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241 |     251       261       271  
                                                                                                                                                                                 243    250                       


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with GLPG_ECOLI | P09391 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:179
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262         
           GLPG_ECOLI    93 AGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLN 271
               SCOP domains d2irvb_ B: GlpG                                                                                                                                                                     SCOP domains
               CATH domains 2irvB00 B:93-271 Rhomboid-like domains                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2irv B  93 AGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLN 271
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
   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, 2)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IRV)

(-) Gene Ontology  (11, 11)

Asymmetric 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GLPG_ECOLI | P09391: 2ic8 2lep 2nrf 2o7l 2xov 2xow 2xtu 2xtv 3b44 3b45 3txt 3ubb 3zeb 3zmh 3zmi 3zmj 3zot 4h1d 4hdd 4njn 4njp 5f5b 5f5d 5f5g 5f5j 5f5k

(-) Related Entries Specified in the PDB File

2ic8 CRYSTAL STRUCTURE OF GLPG