3U96 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YOPHQ357F(CATALYTIC DOMAIN, RESIDUES 163-468) IN COMPLEX WITH PNCS

Authors :   M. C. Ho, S. Ke

Date :   17 Oct 11 (Deposition) - 29 Aug 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Yoph, Ptpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ke, M. C. Ho, N. Zhadin, H. Deng, R. Callender
Investigation Of Catalytic Loop Structure, Dynamics, And Function Relationship Of Yersinia Protein Tyrosine Phosphatase By Temperature-Jump Relaxation Spectroscopy And X-Ray Structural Determination.
J. Phys. Chem. B V. 116 6166 2012
PubMed-ID: 22564106 | Reference-DOI: 10.1021/JP3037846

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE YOPH
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 163-468
	Gene	:	YOP51, YOPH
	Mutation	:	YES
	Organism Scientific	:	YERSINIA ENTEROCOLITICA
	Organism Taxid	:	630
	Synonym	:	VIRULENCE PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CSN	2	Ligand/Ion	N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CSN	2	Ligand/Ion	N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CSN	1	Ligand/Ion	N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CSN	1	Ligand/Ion	N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:229 , 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:481 , HOH A:483	BINDING SITE FOR RESIDUE CSN A 1
2	AC2	SOFTWARE	ARG A:278 , LYS A:342 , SER A:388 , SER A:389 , HOH A:513	BINDING SITE FOR RESIDUE SO4 A 469
3	AC3	SOFTWARE	PHE A:357 , HOH B:72 , PHE B:229 , ILE B:232 , ASP B:356 , PHE 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	BINDING SITE FOR RESIDUE CSN B 1
4	AC4	SOFTWARE	ARG B:278 , LYS B:342 , SER B:388 , SER B:389 , ALA B:390	BINDING SITE FOR RESIDUE SO4 B 2

(no "SS Bond" information available for 3U96)

Asymmetric Unit

No.	Residues
1	Cys A:221	-	Gly A:222
2	Gly A:222	-	Gly A:223
3	Gly B:222	-	Gly B:223

(no "SAP(SNP)/Variant" information available for 3U96)

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, 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 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	A:366-451 -
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	YOPH_YEREN	401-411	1	A:401-411 -

Biological Unit 3 (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 3U96)

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 d3u96a_ A: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.........................hhhhh......eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhhhhhhh..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
                 3u96 A 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDFTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 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 d3u96b_ B: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh..........................hhhhh......eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhh........eee..eeeeeeeeeeeeee..eeeeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.....hhhhhhhhhhhhhhhhhh..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
                 3u96 B 187 SPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDFTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 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

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 '\|'

(no "CATH Domain" information available for 3U96)

(no "Pfam Domain" information available for 3U96)

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
		Cys A:221 - Gly A:222	[ RasMol ]
		Gly A:222 - Gly A:223	[ RasMol ]
		Gly B:222 - Gly B:223	[ RasMol ]

Biological Units
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	3u96
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	3.1.3.48
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(no "Related Entries Specified in the PDB File" available for 3U96)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (9, 9)

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