1YN9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF BACULOVIRUS RNA 5'-PHOSPHATASE COMPLEXED WITH PHOSPHATE

Authors :   A. Changela, A. Martins, S. Shuman, A. Mondragon

Date :   24 Jan 05 (Deposition) - 22 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Rna Triphosphatase, Cysteine Phosphatase, P-Loop, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Changela, A. Martins, S. Shuman, A. Mondragon
Crystal Structure Of Baculovirus Rna Triphosphatase Complexed With Phosphate
J. Biol. Chem. V. 280 17848 2005
PubMed-ID: 15713658 | Reference-DOI: 10.1074/JBC.M500885200
(for further references see the PDB file header)

Molecule 1 - POLYNUCLEOTIDE 5'-PHOSPHATASE
	Chains	:	A, B, C
	EC Number	:	3.1.3.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PTP
	Organism Scientific	:	AUTOGRAPHA CALIFORNICA NUCLEOPOLYHEDROVIRUS
	Organism Taxid	:	46015
	Synonym	:	BVP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	PO4	6	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:119 , THR A:120 , HIS A:121 , ILE A:123 , ASN A:124 , ARG A:125 , ARG A:159 , HOH A:637 , HOH A:675 , HOH A:740	BINDING SITE FOR RESIDUE PO4 A 601
2	AC2	SOFTWARE	THR A:62 , ASN A:63 , THR A:64 , TYR A:67 , THR A:120 , ARG A:125 , HOH A:617 , HOH A:658 , HOH A:668 , HOH A:681 , HOH A:733	BINDING SITE FOR RESIDUE PO4 A 602
3	AC3	SOFTWARE	CYS B:119 , THR B:120 , HIS B:121 , ILE B:123 , ASN B:124 , ARG B:125 , HOH B:662 , HOH B:664	BINDING SITE FOR RESIDUE PO4 B 603
4	AC4	SOFTWARE	THR B:62 , ASN B:63 , THR B:64 , TYR B:67 , THR B:120 , ARG B:125 , HOH B:677 , HOH B:684 , HOH B:713 , HOH B:720 , HOH B:744	BINDING SITE FOR RESIDUE PO4 B 604
5	AC5	SOFTWARE	CYS C:119 , THR C:120 , HIS C:121 , ILE C:123 , ASN C:124 , ARG C:125 , HOH C:629	BINDING SITE FOR RESIDUE PO4 C 605
6	AC6	SOFTWARE	THR C:62 , ASN C:63 , THR C:64 , TYR C:67 , THR C:120 , ARG C:125 , HOH C:641 , HOH C:682	BINDING SITE FOR RESIDUE PO4 C 606

(no "SS Bond" information available for 1YN9)

(no "Cis Peptide Bond" information available for 1YN9)

(no "SAP(SNP)/Variant" information available for 1YN9)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_2	PS50056	Tyrosine specific protein phosphatases family profile.	PTP_NPVAC	97-164	3	A:97-164 B:97-164 C:97-164
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTP_NPVAC	117-127	3	A:117-127 B:117-127 C:117-127

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.	PTP_NPVAC	97-164	1	A:97-164 - -
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTP_NPVAC	117-127	1	A:117-127 - -

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.	PTP_NPVAC	97-164	1	- B:97-164 -
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTP_NPVAC	117-127	1	- B:117-127 -

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.	PTP_NPVAC	97-164	1	- - C:97-164
2	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	PTP_NPVAC	117-127	1	- - C:117-127

(no "Exon" information available for 1YN9)

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:168
 aligned with PTP_NPVAC | P24656 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
            PTP_NPVAC     1 MFPARWHNYLQCGQVIKDSNLICFKTPLRPELFAYVTSEEDVWTAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTVKEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLLI 168
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh...........eeee....hhhhhh...hhhhh.hhhhhhhhh..eeeeee.........hhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:97-164 UniProt: 97-164                    ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yn9 A   1 MFPARWHNYLQCGQVIKDSNLICFKTPLRPELFAYVTSEEDVWTAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTVKEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLLI 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with PTP_NPVAC | P24656 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:169
                             1                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159         
            PTP_NPVAC     - -MFPARWHNYLQCGQVIKDSNLICFKTPLRPELFAYVTSEEDVWTAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTVKEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLLI 168
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh...........eeee....hhhhhh...hhhhh.hhhhhhhhh..eeeeee.........hhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: B:97-164 UniProt: 97-164                    ---- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yn9 B   0 HMFPARWHNYLQCGQVIKDSNLICFKTPLRPELFAYVTSEEDVWTAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTVKEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLLI 168
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

Chain C from PDB  Type:PROTEIN  Length:159
 aligned with PTP_NPVAC | P24656 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       
            PTP_NPVAC     2 FPARWHNYLQCGQVIKDSNLICFKTPLRPELFAYVTSEEDVWTAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTVKEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLLI 168
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------DSPc-1yn9C01 C:42-168                                                                                                           Pfam domains (1)
           Pfam domains (2) ----------------------------------------DSPc-1yn9C02 C:42-168                                                                                                           Pfam domains (2)
           Pfam domains (3) ----------------------------------------DSPc-1yn9C03 C:42-168                                                                                                           Pfam domains (3)
         Sec.struct. author ...hhhhh...........eeee.........--------..hhhhhhhhh..eeeeee.........hhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: C:97-164 UniProt: 97-164                    ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yn9 C   2 FPARWHNYLQCGQVIKDSNLICFKTPLRPELF--------VWTAEQIVKQNPSIGAIIDLTNTSKYYDGVHFLRAGLLYKKIQVPGQTLPPESIVQEFIDTVKEFTEKCPGMLVGVHCTHGINRTGYMVCRYLMHTLGIAPQEAIDRFEKARGHKIERQNYVQDLLI 168
                                    11        21        31 |       -|       51        61        71        81        91       101       111       121       131       141       151       161       
                                                          33       42

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 "SCOP Domain" information available for 1YN9)

(no "CATH Domain" information available for 1YN9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: DSPc (22)

Autographa californica nuclear polyhedrosis virus (AcMNPV) (1)

1a	DSPc-1yn9C01	C:42-168
1b	DSPc-1yn9C02	C:42-168
1c	DSPc-1yn9C03	C:42-168

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PTP_NPVAC | P24656)

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.
	GO:0008138	protein tyrosine/serine/threonine phosphatase activity	Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and 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: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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

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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