1ILD - JenaLib

Title :   OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI N156A ACTIVE SITE MUTANT PH 4.6

Authors :   H. J. Snijder, J. H. Van Eerde, R. L. Kingma, K. H. Kalk, N. Dekker, M. R. Egmond, B. W. Dijkstra

Date :   08 May 01 (Deposition) - 03 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A

Keywords :   Anti-Parallel Beta Barrel, Membrane Phospholipase, Membrane Protein, Serine Hydrolase, N156A, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. J. Snijder, J. H. Van Eerde, R. L. Kingma, K. H. Kalk, N. Dekker, M. R. Egmond, B. W. Dijkstra
Structural Investigations Of The Active-Site Mutant Asn156Ala Of Outer Membrane Phospholipase A: Function Of The Asn-His Interaction In The Catalytic Triad.
Protein Sci. V. 10 1962 2001
PubMed-ID: 11567087 | Reference-DOI: 10.1110/PS.17701
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:122 , THR A:124 , ASP A:125 , TYR A:126 , VAL A:136 , LEU A:225 , THR A:239	BINDING SITE FOR RESIDUE BOG A 500
2	AC2	SOFTWARE	TYR A:42 , TYR A:195 , MPD A:601	BINDING SITE FOR RESIDUE BOG A 501
3	AC3	SOFTWARE	LEU A:118 , MET A:138 , GLY A:139 , TYR A:140 , TYR A:229 , PRO A:230 , MPD A:600 , MPD A:602	BINDING SITE FOR RESIDUE BOG A 502
4	AC4	SOFTWARE	TRP A:78 , ILE A:81 , TRP A:169 , ILE A:199 , TYR A:201 , LEU A:208 , ALA A:210	BINDING SITE FOR RESIDUE BOG A 503
5	AC5	SOFTWARE	GLN A:94 , PHE A:109 , THR A:112 , TYR A:114 , MPD A:602	BINDING SITE FOR RESIDUE BOG A 504
6	AC6	SOFTWARE	HOH A:315 , BOG A:502	BINDING SITE FOR RESIDUE MPD A 600
7	AC7	SOFTWARE	PRO A:175 , TRP A:176 , BOG A:501	BINDING SITE FOR RESIDUE MPD A 601
8	AC8	SOFTWARE	TYR A:140 , BOG A:502 , BOG A:504	BINDING SITE FOR RESIDUE MPD A 602

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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)
	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:257
 aligned with PA1_ECOLI | P0A921 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:257
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       
            PA1_ECOLI    33 AVRGSIIANMLQEHDNPFTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWNRLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF 289
               SCOP domains d1ilda_ A: Outer membrane phospholipase A (OMPLA)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ildA00 A:13-269 Outer membrane phospholipase (ompla).Chain C                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh........ee....eeeeeee.....................eeeeeeeeeeeee......eeeeeeeeeeeee...hhhhh..eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeee........hhhhhh.eeeeeeeee..eeeeeeeee......eeeeeeeeee.....eeeeeeeee...hhhhh....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ild A  13 AVRGSIIANMLQEHDNPFTLYPYDTNYLIYTQTSDLNKEAIASYDWAENARKDEVKFQLSLAFPLWRGILGPNSVLGASYTQKSWWQLSNSEESSPFRETNYEPQLFLGFATDYRFAGWTLRDVEMGYNHDSNGRSDPTSRSWARLYTRLMAENGNWLVEVKPWYVVGNTDDNPDITKYMGYYQLKIGYHLGDAVLSAKGQYNWNTGYGGAELGLSYPITKHVRLYTQVYSGYGESLIDYNFNQTRVGVGVMLNDLF 269
                                    22        32        42        52        62        72        82        92       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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BOG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:149 - Pro A:150	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1ild
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PA1_ECOLI \| P0A921
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.1.32
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description