2X56 - 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 :   2.30

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 (1, 18)

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:132 , GLY A:133 , TYR A:134 , C8E A:1301	BINDING SITE FOR RESIDUE C8E A1293
02	AC2	SOFTWARE	PRO A:61 , TYR A:62	BINDING SITE FOR RESIDUE C8E A1294
03	AC3	SOFTWARE	C8E A:1295 , C8E A:1296	BINDING SITE FOR RESIDUE C8E A 295
04	AC4	SOFTWARE	LEU A:53 , SER A:74 , TYR A:290 , C8E A:295	BINDING SITE FOR RESIDUE C8E A1295
05	AC5	SOFTWARE	LEU A:53 , LYS A:54 , GLY A:55 , GLY A:71 , GLU A:111 , ARG A:138 , C8E A:295	BINDING SITE FOR RESIDUE C8E A1296
06	AC6	SOFTWARE	ALA A:69 , TYR A:112	BINDING SITE FOR RESIDUE C8E A1297
07	AC7	SOFTWARE	TYR A:62 , LEU A:120 , C8E A:1307	BINDING SITE FOR RESIDUE C8E A1298
08	AC8	SOFTWARE	THR A:20 , ALA A:286 , C8E A:1302	BINDING SITE FOR RESIDUE C8E A1300
09	AC9	SOFTWARE	TRP A:199 , C8E A:1293	BINDING SITE FOR RESIDUE C8E A1301
10	BC1	SOFTWARE	THR A:20 , GLY A:21 , MET A:22 , ALA A:51 , C8E A:1300	BINDING SITE FOR RESIDUE C8E A1302
11	BC2	SOFTWARE	ASP A:198	BINDING SITE FOR RESIDUE C8E A1303
12	BC3	SOFTWARE	GLY A:181 , ALA A:192 , PHE A:194 , THR A:227	BINDING SITE FOR RESIDUE C8E A1304
13	BC4	SOFTWARE	PHE A:14 , ILE A:57 , TRP A:59 , LEU A:67	BINDING SITE FOR RESIDUE C8E A1306
14	BC5	SOFTWARE	PHE A:64 , TRP A:119 , C8E A:1298	BINDING SITE FOR RESIDUE C8E A1307
15	BC6	SOFTWARE	SER A:41 , PHE A:215 , GLU A:217	BINDING SITE FOR RESIDUE C8E A1308

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
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Chain A from PDB  Type:PROTEIN  Length:272
 aligned with COLY_YERPE | P17811 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:288
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304        
           COLY_YERPE    25 LIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGGTQTIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF 312
               SCOP domains d2x56a_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2x56A00 A:5-292 OMPT-like                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains Omptin-2x56A01 A:5-292                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeee...eeeeeeeee..........eeeeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee..eeee....eeee.....eeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeee..----------------..hhh.eeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------OMPTIN_1  ---------------------------OMPTIN_2         ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x56 A   5 LIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDE----------------SIGGDAAGISNKNYTVTAGLQYRF 292
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       | -         -    |  274       284        
                                                                                                                                                                                                                                                                                 252              269

Legend:		→ Mismatch	(orange background)
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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 (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.

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	2x56
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