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(-) Description

Title :  OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI
 
Authors :  H. J. Snijder, I. Ubarretxena-Belandia, M. Blaauw, K. H. Kalk, H. M. Ver M. R. Egmond, N Dekker, B. W. Dijkstra
Date :  09 Jul 99  (Deposition) - 25 Oct 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Anti-Parallel Beta Barrel Dimer, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Snijder, I. Ubarretxena-Belandia, M. Blaauw, K. H. Kalk, H. M. Verheij, M. R. Egmond, N. Dekker, B. W. Dijkstra
Structural Evidence For Dimerization-Regulated Activation O An Integral Membrane Phospholipase.
Nature V. 401 717 1999
PubMed-ID: 10537112  |  Reference-DOI: 10.1038/44890
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
    Chains: A, B
    Engineered: YES
    Fragment: RESDIUES 33-45
    Synthetic: YES
 
Molecule 2 - PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
    Chains: C, D
    EC Number: 3.1.1.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2HDS2Ligand/Ion1-HEXADECANOSULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HDS1Ligand/Ion1-HEXADECANOSULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HDS1Ligand/Ion1-HEXADECANOSULFONIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2HDS2Ligand/Ion1-HEXADECANOSULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:147 , SER C:152 , HOH C:285 , HOH C:294 , SER D:106 , HOH D:275BINDING SITE FOR RESIDUE CA C 1
2AC2SOFTWARESER C:106 , ARG D:147 , SER D:152 , HOH D:302BINDING SITE FOR RESIDUE CA C 2
3AC3SOFTWARETYR C:92 , TYR C:114 , HIS C:142 , SER C:144 , ASN C:145 , GLY C:146 , HOH C:285 , TYR D:39 , PHE D:69 , TRP D:98 , PHE D:109 , VAL D:263 , LEU D:265 , HOH D:275BINDING SITE FOR RESIDUE HDS C 270
4AC4SOFTWARETYR C:39 , LEU C:71 , TRP C:98 , PHE C:109 , VAL C:263 , LEU C:265 , TYR D:92 , HIS D:142 , SER D:144 , ASN D:145 , GLY D:146 , HOH D:302BINDING SITE FOR RESIDUE HDS D 270

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QD6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp C:149 -Pro C:150
2Asp D:149 -Pro D:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QD6)

(-) Exons   (0, 0)

(no "Exon" information available for 1QD6)

(-) 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:13
 aligned with PA1_ECOLI | P0A921 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:13
                                    42   
            PA1_ECOLI    33 AVRGSIIANMLQE  45
               SCOP domains d1qd6.1 A:,C: SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 1qd6 A  13 AVRGSIIANMLQE  25
                                    22   


Chain B from PDB  Type:PROTEIN  Length:13
 aligned with PA1_ECOLI | P0A921 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:13
                                    42   
            PA1_ECOLI    33 AVRGSIIANMLQE  45
               SCOP domains d1qd6.2 B:,D: SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 1qd6 B  13 AVRGSIIANMLQE  25
                                    22   


Chain C from PDB  Type:PROTEIN  Length:240
 aligned with PA1_ECOLI | P0A921 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:240
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
            PA1_ECOLI    50 FTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF 289
               SCOP domains d1qd6.1 A:,C: Outer membrane phospholipase A (OMPLA)                                                                                                                                                                                             SCOP domains
               CATH domains 1qd6C00 C:30-269 Outer membrane phospholipase (ompla).Chain C                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....eeeeeee..........hhhhhhh..eeeeeeeeeeeeeee......eeeeeeeeeeeee...hhhhh..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhh.eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeeeeeeeeee..hhhhh..eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qd6 C  30 FTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF 269
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269


Chain D from PDB  Type:PROTEIN  Length:239
 aligned with PA1_ECOLI | P0A921 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:239
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         
            PA1_ECOLI    51 TLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF 289
               SCOP domains d1qd6.2 B:,D: Outer membrane phospholipase A (OMPLA)                                                                                                                                                                                            SCOP domains
               CATH domains 1qd6D00 D:31-269 Outer membrane phospholipase (ompla).Chain C                                                                                                                                                                                   CATH domains
           Pfam domains (1) PLA1-1qd6D01 D:31-266                                                                                                                                                                                                                       --- Pfam domains (1)
           Pfam domains (2) PLA1-1qd6D02 D:31-266                                                                                                                                                                                                                       --- Pfam domains (2)
           Pfam domains (3) PLA1-1qd6D03 D:31-266                                                                                                                                                                                                                       --- Pfam domains (3)
           Pfam domains (4) PLA1-1qd6D04 D:31-266                                                                                                                                                                                                                       --- Pfam domains (4)
         Sec.struct. author ..ee....eeeeeee..........hhhhhhh..eeeeeeeeeeeeeee......eeeeeeeeeeeee...hhhhh..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhh.eeeeeeeee..eeeeeeeee......eeeeeeeeee.....eeeeeeeeee..hhhhh..eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qd6 D  31 TLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF 269
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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 Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: PLA1] (2)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PA1_ECOLI | P0A921)
molecular function
    GO:0052740    1-acyl-2-lysophosphatidylserine acylhydrolase activity    Catalysis of the reaction: 1-acyl-2-lysophosphatidylserine + H2O = sn-glycerol-phosphoserine + a carboxylate.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008970    phosphatidylcholine 1-acylhydrolase activity    Catalysis of the reaction: phosphatidylcholine + H2O = 2-acylglycerophosphocholine + a carboxylate.
    GO:0052739    phosphatidylserine 1-acylhydrolase activity    Catalysis of the reaction: phosphatidylserine + H2O = 2-acyl-sn-glycero-3-phosphoserine + fatty acid.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
    GO:0004620    phospholipase activity    Catalysis of the hydrolysis of a glycerophospholipid.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0045203    integral component of cell outer membrane    The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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:0031230    intrinsic component of cell outer membrane    The component of the cell outer membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

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        PA1_ECOLI | P0A921: 1fw2 1fw3 1ild 1ilz 1im0 1qd5

(-) Related Entries Specified in the PDB File

1qd5 OUTER MEMBRANE PHOSPHOLIPASE A, MONOMERIC FORM