1XXV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   YERSINIA YOPH (RESIDUES 163-468) BINDS PHOSPHONODIFLUOROMETHYL-PHE CONTAINING HEXAPEPTIDE AT TWO SITES

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

Date :   08 Nov 04 (Deposition) - 22 Mar 05 (Release) - 14 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Catalytic Domain, Phosphotyrosine-Binding Sites, Substrate Targeting, Hydrolase (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 - EPIDERMAL GROWTH FACTOR RECEPTOR DERIVED PEPTIDE
	Chains	:	C, D, E, F
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED BY ROBERT ZAMBONI AND MICHAEL GRESSER, MERCK FROSST, MONTREAL
	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, 8)

No.	Name	Count	Type	Full Name
1	FTY	4	Mod. Amino Acid	DEOXY-DIFLUOROMETHELENE-PHOSPHOTYROSINE
2	NH2	4	Mod. Amino Acid	AMINO GROUP

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	FTY	2	Mod. Amino Acid	DEOXY-DIFLUOROMETHELENE-PHOSPHOTYROSINE
2	NH2	2	Mod. Amino Acid	AMINO GROUP

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	FTY	2	Mod. Amino Acid	DEOXY-DIFLUOROMETHELENE-PHOSPHOTYROSINE
2	NH2	2	Mod. Amino Acid	AMINO GROUP

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:229 , ARG A:230 , ASP A:231 , ILE A:232 , ASP A:356 , GLN A:357 , CYS A:403 , ARG A:404 , ALA A:405 , GLY A:406 , VAL A:407 , GLY A:408 , ARG A:409 , GLN A:446 , HOH A:632 , HOH A:745 , HOH B:705 , NH2 C:107 , HOH C:624	BINDING SITE FOR CHAIN C OF EPIDERMAL GROWTH FACTOR RECEPTOR DERIVED PEPTIDE
2	AC2	SOFTWARE	ARG A:278 , ARG A:295 , LYS A:342 , THR A:343 , MET A:382 , LYS A:386 , SER A:388 , SER A:389 , HOH A:774 , SER B:468 , NH2 D:7 , HOH D:539 , HOH D:540 , HOH D:542	BINDING SITE FOR CHAIN D OF EPIDERMAL GROWTH FACTOR RECEPTOR DERIVED PEPTIDE
3	AC3	SOFTWARE	HOH A:749 , PHE B:229 , ARG B:230 , ASP B:231 , ILE B:232 , ASP B:356 , GLN B:357 , CYS B:403 , ARG B:404 , ALA B:405 , GLY B:406 , VAL B:407 , GLY B:408 , ARG B:409 , GLN B:446 , NH2 E:107 , HOH E:783	BINDING SITE FOR CHAIN E OF EPIDERMAL GROWTH FACTOR RECEPTOR DERIVED PEPTIDE
4	AC4	SOFTWARE	SER A:468 , ARG B:278 , ARG B:295 , LYS B:342 , THR B:343 , ILE B:344 , SER B:345 , LYS B:386 , SER B:388 , SER B:389 , HOH B:709 , NH2 F:7 , HOH F:642 , HOH F:644 , HOH F:818	BINDING SITE FOR CHAIN F OF EPIDERMAL GROWTH FACTOR RECEPTOR DERIVED PEPTIDE

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

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

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

Asymmetric Unit (2, 4)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

(no "Exon" information available for 1XXV)

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:282
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:282
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466  
           YOPH_YEREN   187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d1xxva1 A:187-468 Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xxvA00 A:187-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..........................hhhhh......eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.............eee.....hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:366-451 UniProt: 366-451                                    ----------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xxv A 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with YOPH_YEREN | P15273 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:282
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466  
           YOPH_YEREN   187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCCRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
               SCOP domains d1xxvb1 B:187-468 Protein-tyrosine phosphatase YopH, catalytic domain                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xxvB00 B:187-468 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ------------------------------------Y_phosphatase-1xxvB01 B:223-459                                                                                                                                                                                                              --------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Y_phosphatase-1xxvB02 B:223-459                                                                                                                                                                                                              --------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.....................................eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.............eee.....hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:366-451 UniProt: 366-451                                    ----------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xxv B 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 468
                                   196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1xxv C 103 DEyLx 107
                              | |
                            105-FTY
                              107-NH2

Chain D from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1xxv D   1 DADEyLx   7
                                | |
                                | |
                                5-FTY
                                  7-NH2

Chain E from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1xxv E 103 DEyLx 107
                              | |
                              | |
                            105-FTY
                              107-NH2

Chain F from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1xxv F   1 DADEyLx   7
                                | |
                                | |
                                5-FTY
                                  7-NH2

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	1xxvA00	A:187-468
1b	1xxvB00	B:187-468

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase (93)

Yersinia enterocolitica (6)

1a	Y_phosphatase-1xxvB01	B:223-459
1b	Y_phosphatase-1xxvB02	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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Biological Units
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	1xxv
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1qz0	CRYSTAL STRUCTURE OF THE YERSINIA PESTIS PHOSPHATASE YOPH IN COMPLEX WITH A PHOSPHOTYROSYL MIMETIC-CONTAINING HEXAPEPTIDE
1xxp	COMPANION STRUCTURE OF YOPH (RESIDUES 163-468) C403S BOUND TO A PHOSPHOTYROSYL-CONTAINING HEXAPEPTIDE

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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