1D1Q - JenaLib

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Title :   CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE SUBSTRATE PNPP

Authors :   S. Wang, L. Tabernero, M. Zhang, E. Harms, R. L. Van Etten, C. V. Staufac

Date :   20 Sep 99 (Deposition) - 08 Mar 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Beta-Alpha-Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Wang, L. Tabernero, M. Zhang, E. Harms, R. L. Van Etten, C. V. Stauffacher
Crystal Structures Of A Low-Molecular Weight Protein Tyrosine Phosphatase From Saccharomyces Cerevisiae And Its Complex With The Substrate P-Nitrophenyl Phosphate.
Biochemistry V. 39 1903 2000
PubMed-ID: 10684639 | Reference-DOI: 10.1021/BI991348D
(for further references see the PDB file header)

Molecule 1 - TYROSINE PHOSPHATASE (E.C.3.1.3.48)
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	4NP	1	Ligand/Ion	4-NITROPHENYL PHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	4NP	1	Ligand/Ion	4-NITROPHENYL PHOSPHATE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	4NP	-1	Ligand/Ion	4-NITROPHENYL PHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:13 , LEU B:14 , GLY B:15 , ASN B:16 , PHE B:17 , CYS B:18 , ARG B:19 , SER B:20 , HOH B:415 , HOH B:426	BINDING SITE FOR RESIDUE PO4 B 402
2	AC2	SOFTWARE	GLU A:3 , ALA A:13 , LEU A:14 , GLY A:15 , ASN A:16 , PHE A:17 , CYS A:18 , ARG A:19 , ASP A:132 , TRP A:134 , HOH A:457 , TYR B:51 , HOH B:432	BINDING SITE FOR RESIDUE 4NP A 401
3	AC3	SOFTWARE	ILE A:64 , GLN A:67 , GLN A:139 , HOH A:436 , HOH A:469 , HOH A:490 , HOH A:491 , TRP B:134 , TYR B:135	BINDING SITE FOR RESIDUE GOL B 403

(no "SS Bond" information available for 1D1Q)

(no "Cis Peptide Bond" information available for 1D1Q)

(no "SAP(SNP)/Variant" information available for 1D1Q)

(no "PROSITE Motif" information available for 1D1Q)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPR073C	1	YPR073C.1	XVI:692415-691930	486	PPAL_YEAST	1-161	161	2	A:2-160 B:3-160	159 158

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
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Chain A from PDB  Type:PROTEIN  Length:159
 aligned with PPAL_YEAST | P40347 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:159
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152         
           PPAL_YEAST     3 IEKPKISVAFICLGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 161
               SCOP domains d1d1qa_ A: Tyrosine phosphatase                                                                                                                                 SCOP domains
               CATH domains 1d1qA00 A:2-160  [code=3.40.50.270, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee....hhhhhhhhhhhhhhhhh.hhh.eeeeeeee..........hhhhhhhhhhh...........hhhhhhh..eeee.hhhhhhhhhhhh......eeee.hhhh................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-160 UniProt: 1-161 [INCOMPLETE]                                                                                                              Transcript 1
                 1d1q A   2 IEKPKISVAFIALGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with PPAL_YEAST | P40347 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153        
           PPAL_YEAST     4 EKPKISVAFICLGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 161
               SCOP domains d1d1qb_ B: Tyrosine phosphatase                                                                                                                                SCOP domains
               CATH domains 1d1qB00 B:3-160  [code=3.40.50.270, no name defined]                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....hhhhhhhhhhhhhhhhh.hhh.eeeeeeee..........hhhhhhhhhhh.............hhhhhh.eeee.hhhhhhhhhhhh......eeee.hhhh................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-160 UniProt: 1-161 [INCOMPLETE]                                                                                                             Transcript 1
                 1d1q B   3 EKPKISVAFIALGNFCRSPMAEAIFKHEVEKANLENRFNKIDSFGTSNYHVGESPDHRTVSICKQHGVKINHKGKQIKTKHFDEYDYIIGMDESNINNLKKIQPEGSKAKVCLFGDWNTNDGTVQTIIEDPWYGDIQDFEYNFKQITYFSKQFLKKEL 160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.270, no name defined] (36)

Baker's yeast (Saccharomyces cerevisiae) (3)

1a	1d1qB00	B:3-160
1b	1d1qA00	A:2-160

(no "Pfam Domain" information available for 1D1Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPAL_YEAST | P40347)

molecular function
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
	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: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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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1d1p	STRUCTURE OF WILD-TYPE LTP1 COMPLEXED WITH HEPES

Description

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Ligands, Modified Residues, Ions (3, 3)

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