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Asym./Biol. Unit (Jmol Viewer)

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Title :   YEAST INORGANIC PYROPHOSPHATASE VARIANT D120E WITH MAGNESIUM AND PHOSPHATE

Authors :   E. Oksanen, A. K. Ahonen, H. Tuominen, V. Tuominen, R. Lahti, A. Goldman, P. Heikinheimo

Date :   02 Oct 06 (Deposition) - 13 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Inorganic Pyrophosphatase, Mechanism, X-Ray Crystallography, Structure-Function, Mutagenesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Oksanen, A. K. Ahonen, H. Tuominen, V. Tuominen, R. Lahti, A. Goldman, P. Heikinheimo
A Complete Structural Description Of The Catalytic Cycle Of Yeast Pyrophosphatase.
Biochemistry V. 46 1228 2007
PubMed-ID: 17260952 | Reference-DOI: 10.1021/BI0619977
(for further references see the PDB file header)

Molecule 1 - INORGANIC PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKW9
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IPP1
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MG	5	Ligand/Ion	MAGNESIUM ION
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:115 , GLU A:120 , ASP A:152 , HOH A:339 , HOH A:481 , HOH A:503	BINDING SITE FOR RESIDUE MG A 287
2	AC2	SOFTWARE	PO4 A:289 , HOH A:465 , HOH A:490 , HOH A:498	BINDING SITE FOR RESIDUE MG A 288
3	AC3	SOFTWARE	ASP B:115 , GLU B:120 , ASP B:152 , HOH B:294 , HOH B:578 , HOH B:579	BINDING SITE FOR RESIDUE MG B 287
4	AC4	SOFTWARE	MG B:289 , PO4 B:290 , HOH B:451 , HOH B:452 , HOH B:487 , HOH B:564 , HOH B:588	BINDING SITE FOR RESIDUE MG B 288
5	AC5	SOFTWARE	MG B:288 , HOH B:355 , HOH B:452 , HOH B:487 , HOH B:505 , HOH B:582 , HOH B:588	BINDING SITE FOR RESIDUE MG B 289
6	AC6	SOFTWARE	ARG B:78 , ASP B:147 , TYR B:192 , LYS B:193 , MG B:288 , HOH B:334 , HOH B:336 , HOH B:451 , HOH B:452 , HOH B:564 , HOH B:579 , HOH B:588	BINDING SITE FOR RESIDUE PO4 B 290
7	AC7	SOFTWARE	ARG A:78 , ASP A:147 , TYR A:192 , LYS A:193 , MG A:288 , HOH A:358 , HOH A:414 , HOH A:461 , HOH A:490 , HOH A:498 , HOH A:503	BINDING SITE FOR RESIDUE PO4 A 289
8	AC8	SOFTWARE	ASN B:186 , SER B:206 , GLY B:207 , HOH B:396 , HOH B:429 , HOH B:462	BINDING SITE FOR RESIDUE MPD B 291

(no "SS Bond" information available for 2IK6)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:84	-	Pro A:85
2	Phe B:84	-	Pro B:85

(no "SAP(SNP)/Variant" information available for 2IK6)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PPASE	PS00387	Inorganic pyrophosphatase signature.	IPYR_YEAST	116-122	2	A:115-121 B:115-121

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR011C	1	YBR011C.1	II:257973-257110	864	IPYR_YEAST	1-287	287	2	A:1-282 (gaps) B:1-282	282 282

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:268
 aligned with IPYR_YEAST | P00817 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:282
                                    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  
           IPYR_YEAST     2 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASPKADAPIDKSIDKWFFI 283
               SCOP domains d2ik6a_ A: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2ik6A00 A:1-282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee........eeeeee..eee........eeehhh.eeeeeeee.......eee........eee.ee..ee....ee........eeee........----------......eeee..........eeeeeeeeeeeeee..eeeeeeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh....ee.hhhh.eehhhhhhhhhhhhhhhhhhhh.----..................hhhhhh............hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-282 (gaps) UniProt: 1-287 [INCOMPLETE]                                                                                                                                                                                                                                  Transcript 1
                 2ik6 A   1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDP----------GDNDPIEVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAG----SKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 282
                                    10        20        30        40        50        60        70        80        90       100  |      -   |   120       130       140       150       160       170       180       190       200       210       220       230 |    |240       250       260       270       280  
                                                                                                                                103        114                                                                                                                   232  237

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with IPYR_YEAST | P00817 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:282
                                    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  
           IPYR_YEAST     2 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASPKADAPIDKSIDKWFFI 283
               SCOP domains d2ik6b_ B: Inorganic pyrophosphatase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2ik6B00 B:1-282 Inorganic Pyrophosphatase                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee......eeeeee..eee........eee....eeeeeeee.......eee........eee.ee..ee....ee........eeee..........ee....ee......eeee..........eeeeeeeeee.eee..ee..eeeeee....hhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh....ee.hhhh.eehhhhhhhhhhhhhhhhhhhh......................hhhhh......eee.....hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------PPASE  ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-282 UniProt: 1-287 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 1
                 2ik6 B   1 TYTTRQIGAKNTLEYKVYIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIEVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSSDSKGIDLTNVTLPDTPTYSKAASDAIPPASLKADAPIDKSIDKWFFI 282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Inorganic pyrophosphatase (69)

Family: Inorganic pyrophosphatase (56)

Protein domain: Inorganic pyrophosphatase (41)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (19)

1a	d2ik6a_	A:
1b	d2ik6b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Inorganic Pyrophosphatase (59)

Homologous Superfamily: Inorganic Pyrophosphatase (59)

Baker's yeast (Saccharomyces cerevisiae) (17)

1a	2ik6A00	A:1-282
1b	2ik6B00	B:1-282

(no "Pfam Domain" information available for 2IK6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IPYR_YEAST | P00817)

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:0004427	inorganic diphosphatase activity	Catalysis of the reaction: diphosphate + H(2)O = H(+) + 2 phosphate.
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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