2X55 - JenaLib

Title :   YERSINIA PESTIS PLASMINOGEN ACTIVATOR PLA (NATIVE)

Authors :   E. Eren, M. Murphy, J. Goguen, B. Van Den Berg

Date :   05 Feb 10 (Deposition) - 28 Jul 10 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Transmembrane, Aspartyl Protease, Cell Outer Membrane, Omptin, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Eren, M. Murphy, J. Goguen, B. Van Den Berg
An Active Site Water Network In The Plasminogen Activator Pla From Yersinia Pestis
Structure V. 18 809 2010
PubMed-ID: 20637417 | Reference-DOI: 10.1016/J.STR.2010.03.013

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 25)

Sites (23, 23)

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	C8E A:1303	BINDING SITE FOR RESIDUE C8E A1293
02	AC2	SOFTWARE	GLY A:55 , GLY A:71 , ASN A:110 , TYR A:112 , ARG A:138	BINDING SITE FOR RESIDUE C8E A1295
03	AC3	SOFTWARE	ALA A:18 , LEU A:53 , SER A:74 , LEU A:288 , TYR A:290 , C8E A:1307	BINDING SITE FOR RESIDUE C8E A1296
04	AC4	SOFTWARE	TRP A:59 , PRO A:61 , TYR A:62	BINDING SITE FOR RESIDUE C8E A1297
05	AC5	SOFTWARE	GLY A:133 , ILE A:177 , TRP A:199	BINDING SITE FOR RESIDUE C8E A1298
06	AC6	SOFTWARE	THR A:20 , ASN A:49 , C8E A:1306 , C8E A:1307	BINDING SITE FOR RESIDUE C8E A1300
07	AC7	SOFTWARE	C8E A:1315	BINDING SITE FOR RESIDUE C8E A1301
08	AC8	SOFTWARE	TYR A:62 , LEU A:120 , C8E A:1311	BINDING SITE FOR RESIDUE C8E A1302
09	AC9	SOFTWARE	ARG A:70 , GLY A:71 , TYR A:112 , C8E A:1293	BINDING SITE FOR RESIDUE C8E A1303
10	BC1	SOFTWARE	LEU A:179 , ALA A:192 , PHE A:194 , THR A:227	BINDING SITE FOR RESIDUE C8E A1304
11	BC2	SOFTWARE	GLU A:29 , HIS A:208 , GLU A:217 , C8E A:1314	BINDING SITE FOR RESIDUE C8E A1305
12	BC3	SOFTWARE	VAL A:284 , ALA A:286 , C8E A:1300	BINDING SITE FOR RESIDUE C8E A1306
13	BC4	SOFTWARE	ALA A:18 , THR A:20 , VAL A:241 , ALA A:286 , GLY A:287 , C8E A:1296 , C8E A:1300 , C8E A:1313	BINDING SITE FOR RESIDUE C8E A1307
14	BC5	SOFTWARE	PHE A:245	BINDING SITE FOR RESIDUE C8E A1308
15	BC6	SOFTWARE	C8E A:1312	BINDING SITE FOR RESIDUE C8E A1309
16	BC7	SOFTWARE	ILE A:130 , ILE A:177 , GLY A:178 , LEU A:179	BINDING SITE FOR RESIDUE C8E A1310
17	BC8	SOFTWARE	PHE A:64 , VAL A:116 , TRP A:119 , LEU A:120 , C8E A:1302	BINDING SITE FOR RESIDUE C8E A1311
18	BC9	SOFTWARE	PHE A:14 , C8E A:1309	BINDING SITE FOR RESIDUE C8E A1312
19	CC1	SOFTWARE	PHE A:242 , C8E A:1307	BINDING SITE FOR RESIDUE C8E A1313
20	CC2	SOFTWARE	ASP A:86 , C8E A:1305	BINDING SITE FOR RESIDUE C8E A1314
21	CC3	SOFTWARE	TYR A:126 , C8E A:1301	BINDING SITE FOR RESIDUE C8E A1315
22	CC4	SOFTWARE	TYR A:62 , SER A:63 , ASN A:89 , ASN A:91	BINDING SITE FOR RESIDUE SO4 A1316
23	CC5	SOFTWARE	ARG A:171 , SER A:173 , ARG A:201 , HIS A:203 , HOH A:2155 , HOH A:2200	BINDING SITE FOR RESIDUE SO4 A1317

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

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:274
 aligned with COLY_YERPE | P17811 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:290
                                                                                                                                                                                                                                                                                                                          312 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        |-
           COLY_YERPE    24 QLIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGGTQTIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF-   -
               SCOP domains d2x55a_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2x55A00 A:4-293 OMPT-like                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains Omptin-2x55A01 A:4-292                                                                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author ..........eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeee......................eeeeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee...................eeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeee.hhheeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeee..----------------..hhh.eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------OMPTIN_1  ---------------------------OMPTIN_2         ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x55 A   4 QLIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDE----------------SIGGDAAGISNKNYTVTAGLQYRFG 293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        |-         -     | 273       283       293
                                                                                                                                                                                                                                                                                  252              269

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 (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (COLY_YERPE | P17811)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	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.
biological process
	GO:0042730	fibrinolysis	A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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: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: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
		C8E	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x55)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2x55
		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
	COLY_YERPE \| P17811
		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)
	3.4.23.48
		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