1XXP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   YERSINIA YOPH (RESIDUES 163-468) C403S BINDS PHOSPHOTYROSYL PEPTIDE AT TWO SITES

Authors :   M. I. Ivanov, J. A. Stuckey, H. L. Schubert, M. A. Saper, J. B. Bliska

Date :   07 Nov 04 (Deposition) - 22 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D  (1x)
Biol. Unit 2: B,E,F  (1x)

Keywords :   Peptide Binds At Site Remote From Catalytic Site. Important For Protein Localization In Infected Cell. , Hydrolase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. I. Ivanov, J. A. Stuckey, H. L. Schubert, M. A. Saper, J. B. Bliska
Two Substrate-Targeting Sites In The Yersinia Protein Tyrosine Phosphatase Co-Operate To Promote Bacterial Virulence
Mol. Microbiol. V. 55 1346 2005
PubMed-ID: 15720545 | Reference-DOI: 10.1111/J.1365-2958.2005.04477.X

Molecule 1 - PROTEIN-TYROSINE PHOSPHATASE YOPH
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21/DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 163-468
	Gene	:	YOPH, YOP51
	Mutation	:	YES
	Organism Scientific	:	YERSINIA ENTEROCOLITICA
	Organism Taxid	:	630
	Synonym	:	VIRULENCE PROTEIN

Molecule 2 - HEXAPEPTIDE ASP-ALA-ASP-GLU-PTR-CLE
	Chains	:	C, D, E, F
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A		C	D
Biological Unit 2 (1x)	:		B			E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NH2	2	Mod. Amino Acid	AMINO GROUP
2	PTR	4	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:278 , ARG A:295 , LYS A:342 , THR A:343 , SER A:345 , MET A:382 , TYR A:383 , LYS A:386 , SER A:388 , SER A:389 , HOH C:88 , HOH C:90	BINDING SITE FOR CHAIN C OF HEXAPEPTIDE ASP-ALA- ASP-GLU-PTR-CLE
2	AC2	SOFTWARE	PHE A:229 , ASP A:356 , GLN A:357 , SER A:403 , ARG A:404 , ALA A:405 , GLY A:406 , VAL A:407 , GLY A:408 , ARG A:409 , GLN A:446	BINDING SITE FOR CHAIN D OF HEXAPEPTIDE ASP-ALA- ASP-GLU-PTR-CLE
3	AC3	SOFTWARE	SER A:468 , ARG B:278 , ARG B:295 , LYS B:342 , THR B:343 , SER B:345 , MET B:382 , TYR B:383 , LYS B:386 , SER B:388 , SER B:389 , HOH E:91	BINDING SITE FOR CHAIN E OF HEXAPEPTIDE ASP-ALA- ASP-GLU-PTR-CLE
4	AC4	SOFTWARE	PHE B:229 , ASP B:231 , ASP B:356 , GLN B:357 , SER B:403 , ARG B:404 , ALA B:405 , GLY B:406 , VAL B:407 , GLY B:408 , ARG B:409 , GLN B:446	BINDING SITE FOR CHAIN F OF HEXAPEPTIDE ASP-ALA- ASP-GLU-PTR-CLE

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

(no "Cis Peptide Bond" information available for 1XXP)

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	YOPH_YEREN	186-451	2	A:186-451 B:186-451
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	YOPH_YEREN	366-451	2	A:366-451 B:366-451
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	YOPH_YEREN	401-411	2	A:401-411 B:401-411

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	YOPH_YEREN	186-451	1	A:186-451 -
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	YOPH_YEREN	366-451	1	A:366-451 -
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	YOPH_YEREN	401-411	1	A:401-411 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_PTP	PS50055	PTP type protein phosphatase family profile.	YOPH_YEREN	186-451	1	- B:186-451
2	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	YOPH_YEREN	366-451	1	- B:366-451
3	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	YOPH_YEREN	401-411	1	- B:401-411

(no "Exon" information available for 1XXP)

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:287
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:287
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       
           YOPH_YEREN   182 APSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains ----d1xxpa1 A:186-468 Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                       SCOP domains
               CATH domains 1xxpA00 A:182-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhh.....................................eeeeee..eeeeee......hhhhhhhhhhhh....eee..hhhhhhh............eee..eee...eeeeee.....eeeeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhh.......hhhhhhhhhhhhh......hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----TYR_PHOSPHATASE_PTP  PDB: A:186-451 UniProt: 186-451                                                                                                                                                                                                                      ----------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:366-451 UniProt: 366-451                                    ----------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxp A 182 APSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHSRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:283
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465   
           YOPH_YEREN   186 VSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d1xxpb1 B:186-468 Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                       SCOP domains
               CATH domains 1xxpB00 B:186-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) -------------------------------------Y_phosphatase-1xxpB01 B:223-459                                                                                                                                                                                                              --------- Pfam domains (1)
           Pfam domains (2) -------------------------------------Y_phosphatase-1xxpB02 B:223-459                                                                                                                                                                                                              --------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....................................eeeeee..eeeeee......hhhhhhhhhhhh....eee..hhhhhhh............eee..eee...eeeeee.....eeeeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_PTP  PDB: B:186-451 UniProt: 186-451                                                                                                                                                                                                                      ----------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:366-451 UniProt: 366-451                                    ----------------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxp B 186 VSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHSRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1xxp C 102 ADEyLx 107
                               | |
                             105-PTR
                               107-NH2

Chain D from PDB  Type:PROTEIN  Length:1
                                 
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
                 Transcript - Transcript
                 1xxp D 102 y 105
                                  |
                                  |
                                105-PTR

Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1xxp E 102 ADEyLx 107
                               | |
                               | |
                             105-PTR
                               107-NH2

Chain F from PDB  Type:PROTEIN  Length:1
                                 
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
                 Transcript - Transcript
                 1xxp F 102 y 105
                                  |
                                  |
                                105-PTR

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Protein-Tyrosine Phosphatase; Chain A (262)

Homologous Superfamily: Protein tyrosine phosphatase superfamily (228)

Yersinia enterocolitica. Organism_taxid: 630. (7)

1a	1xxpB00	B:186-468
1b	1xxpA00	A:182-468

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase (93)

Yersinia enterocolitica (6)

1a	Y_phosphatase-1xxpB01	B:223-459
1b	Y_phosphatase-1xxpB02	B:223-459

Asymmetric Unit(hide GO term definitions)

Chain A,B (YOPH_YEREN | P15273)

molecular function
	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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xxp)

Biological Units
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Jmol
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Access by PDB/NDB ID
	1xxp
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1qz0	LIKE 1XXV BUT FROM OTHER RESEARCHERS
1xxv	COMPANION STRUCTURE OF ACTIVE YOPH BOUND TO A PHOSPHOTYROSYL MIMETIC HEXAPEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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