1KA1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE PAPASE HAL2P COMPLEXED WITH CALCIUM AND MAGNESIUM IONS AND REACTION SUBSTRATE: PAP

Authors :   S. Patel, A. Albert, T. L. Blundell

Date :   31 Oct 01 (Deposition) - 07 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Nucleotidase, Salt Tolerance, Inositol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Patel, M. Martinez-Ripoll, T. L. Blundell, A. Albert
Structural Enzymology Of Li(+)-Sensitive/Mg(2+)-Dependent Phosphatases.
J. Mol. Biol. V. 320 1087 2002
PubMed-ID: 12126627 | Reference-DOI: 10.1016/S0022-2836(02)00564-8
(for further references see the PDB file header)

Molecule 1 - HALOTOLERANCE PROTEIN HAL2
	Chains	:	A
	EC Number	:	3.1.3.7
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	PRS-421-HAL2
	Expression System Strain	:	RS1051
	Expression System Taxid	:	4932
	Expression System Vector Type	:	MULTI-COPY PLASMID
	Gene	:	HAL2
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	HAL2P, 3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE, PHOSPHOADENYLATE 3'-NUCLEOTIDASE, 3'- PHOSPHOADENYLYLSULFATE 3'-PHOSPHATASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	A3P	1	Ligand/Ion	ADENOSINE-3'-5'-DIPHOSPHATE
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	CA	1	Ligand/Ion	CALCIUM ION
4	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:72 , ASP A:142 , ILE A:144 , A3P A:601 , HOH A:603 , HOH A:613	BINDING SITE FOR RESIDUE CA A 401
2	AC2	SOFTWARE	ASP A:142 , ASP A:145 , ASP A:294 , A3P A:601 , HOH A:639	BINDING SITE FOR RESIDUE MG A 501
3	AC3	SOFTWARE	GLU A:72 , ASP A:142 , ILE A:144 , ASP A:145 , GLY A:146 , THR A:147 , GLY A:240 , HIS A:241 , ASP A:263 , SER A:264 , LYS A:267 , ARG A:281 , TYR A:288 , ASP A:294 , CA A:401 , MG A:501 , HOH A:606 , HOH A:613 , HOH A:627 , HOH A:632 , HOH A:639 , HOH A:640 , HOH A:675 , HOH A:797 , HOH A:815 , HOH A:998 , HOH A:1027	BINDING SITE FOR RESIDUE A3P A 601
4	AC4	SOFTWARE	MET A:313 , GLU A:314 , CYS A:349 , GLN A:353 , HOH A:807 , HOH A:1005	BINDING SITE FOR RESIDUE BME A 602

(no "SS Bond" information available for 1KA1)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:336	-	Pro A:337

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MET22_YEAST_001 *	N	40	S	MET22_YEAST	---	---	A	N	40	S
2	UniProt	VAR_MET22_YEAST_002 *	K	61	M	MET22_YEAST	---	---	A	K	61	M
3	UniProt	VAR_MET22_YEAST_003 *	N	63	S	MET22_YEAST	---	---	A	N	63	S
4	UniProt	VAR_MET22_YEAST_004 *	I	308	V	MET22_YEAST	---	---	A	I	308	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_1	PS00629	Inositol monophosphatase family signature 1.	MET22_YEAST	139-152	1	A:139-152
2	IMP_2	PS00630	Inositol monophosphatase family signature 2.	MET22_YEAST	293-307	1	A:293-307

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOL064C	1	YOL064C.1	XV:207176-206103	1074	MET22_YEAST	1-357	357	1	A:2-355	354

Asymmetric/Biological 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:354
 aligned with MET22_YEAST | P32179 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:354
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351    
          MET22_YEAST     2 ALERELLVATQAVRKASLLTKRIQSEVISHKDSTTITKNDNSPVTTGDYAAQTIIINAIKSNFPDDKVVGEESSSGLSDAFVSGILNEIKANDEVYNKNYKKDDFLFTNDQFPLKSLEDVRQIIDFGNYEGGRKGRFWCLDPIDGTKGFLRGEQFAVCLALIVDGVVQLGCIGCPNLVLSSYGAQDLKGHESFGYIFRAVRGLGAFYSPSSDAESWTKIHVRHLKDTKDMITLEGVEKGHSSHDEQTAIKNKLNISKSLHLDSQAKYCLLALGLADVYLRLPIKLSYQEKIWDHAAGNVIVHEAGGIHTDAMEDVPLDFGNGRTLATKGVIASSGPRELHDLVVSTSCDVIQSR 355
               SCOP domains d1ka1a_ A: 3';5'-adenosine bisphosphatase, PAP phosphatase                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1ka1A01 A:2-220 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                                                                                                           1ka1A02 A:221-355  [code=3.40.190.80, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeehhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhh.........eeeeeeeeehhhhhhh....eeeeeeee..eeeeeeeee...hhhhhh...........eeeeee....eeeee.......ee.......hhhh.eeee.......hhhhhhhhhhhh...eeee...hhhhhhhhhh...eeee.........hhhhhhhhhhhhhhh..eee....................eeee..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------S--------------------M-S----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V----------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------IMP_1         --------------------------------------------------------------------------------------------------------------------------------------------IMP_2          ------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-355 UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                 Transcript 1
                 1ka1 A   2 ALERELLVATQAVRKASLLTKRIQSEVISHKDSTTITKNDNSPVTTGDYAAQTIIINAIKSNFPDDKVVGEESSSGLSDAFVSGILNEIKANDEVYNKNYKKDDFLFTNDQFPLKSLEDVRQIIDFGNYEGGRKGRFWCLDPIDGTKGFLRGEQFAVCLALIVDGVVQLGCIGCPNLVLSSYGAQDLKGHESFGYIFRAVRGLGAFYSPSSDAESWTKIHVRHLKDTKDMITLEGVEKGHSSHDEQTAIKNKLNISKSLHLDSQAKYCLLALGLADVYLRLPIKLSYQEKIWDHAAGNVIVHEAGGIHTDAMEDVPLDFGNGRTLATKGVIASSGPRELHDLVVSTSCDVIQSR 355
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

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 "Pfam Domain" information available for 1KA1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MET22_YEAST | P32179)

molecular function
	GO:0008441	3'(2'),5'-bisphosphate nucleotidase activity	Catalysis of the reaction: adenosine 3',5'-bisphosphate + H2O = adenosine 5'-phosphate + phosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0042538	hyperosmotic salinity response	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, an increase in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
	GO:0006790	sulfur compound metabolic process	The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:336 - Pro A:337	[ RasMol ]

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	1ka1
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	3.1.3.7
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UniProtKB/Swiss-Prot
	MET22_YEAST \| P32179	:	1k9y 1k9z 1ka0 1qgx

1k9y	THE PAPASE HAL2P COMPLEXED WITH MAGNESIUM IONS AND REACTION PRODUCTS: AMP AND INORGANIC PHOSPHATE
1k9z	THE PAPASE HAL2P COMPLEXED WITH ZINC IONS
1ka0	THE PAPASE HAL2P COMPLEXED WITH A SODIUM ION AND THE REACTION PRODUCT AMP
1qgx	1QGX IS COMPLEXED WITH TWO MAGNESIUM IONS AND A LITHIUM ION AND REACTION PRODUCTS AMP AND INORGANIC PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (2, 2)

Exons (1, 1)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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