2QB6 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   SACCHAROMYCES CEREVISIAE CYTOSOLIC EXOPOLYPHOSPHATASE, SULFATE COMPLEX

Authors :   S. A. White, E. Ugochukwu

Date :   16 Jun 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   A/B/A Structure, Dhh Family Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, A. L. Lovering, O. C. Mather, T. W. Young, S. A. White
The Crystal Structure Of The Cytosolic Exopolyphosphatase From Saccharomyces Cerevisiae Reveals The Basis For Substrate Specificity.
J. Mol. Biol. V. 371 1007 2007
PubMed-ID: 17599355 | Reference-DOI: 10.1016/J.JMB.2007.05.066

Molecule 1 - EXOPOLYPHOSPHATASE
	Atcc	:	204511
	Chains	:	A, B
	EC Number	:	3.6.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PPX1, YHR201C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	S288C
	Synonym	:	EXOPOLYPASE, METAPHOSPHATASE

		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 (5, 10)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	MN	2	Ligand/Ion	MANGANESE (II) ION
5	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	-1	Ligand/Ion	GLYCEROL
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:41 , ASP A:127 , HIS A:148 , HOH A:939 , HOH A:948	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	ASP B:41 , ASP B:127 , HIS B:148 , HOH B:577 , HOH B:578	BINDING SITE FOR RESIDUE MN B 401
03	AC3	SOFTWARE	HIS A:149 , LYS A:268 , ARG A:381 , LYS A:382 , EDO A:803 , HOH A:1051 , HOH A:1062 , HOH A:1211	BINDING SITE FOR RESIDUE SO4 A 501
04	AC4	SOFTWARE	SER A:258 , SER A:260 , HOH A:914 , SER B:62 , GLU B:63 , GLU B:64 , LYS B:66 , HOH B:517 , HOH B:686 , HOH B:803	BINDING SITE FOR RESIDUE SO4 A 502
05	AC5	SOFTWARE	LYS B:268 , ARG B:381 , LYS B:382 , HOH B:643 , HOH B:790	BINDING SITE FOR RESIDUE SO4 B 501
06	AC6	SOFTWARE	GLU A:80 , ASP A:81 , LEU A:84 , ASP A:261 , LYS A:264	BINDING SITE FOR RESIDUE ACT A 805
07	AC7	SOFTWARE	MET A:206 , HOH A:821 , HOH A:857 , HOH A:862 , HOH A:949 , MET B:206	BINDING SITE FOR RESIDUE EDO A 801
08	AC8	SOFTWARE	HIS A:148 , HIS A:149 , PHE A:150 , VAL A:163 , LYS A:164 , VAL A:165 , LYS A:382 , HOH A:915 , HOH A:997	BINDING SITE FOR RESIDUE EDO A 802
09	AC9	SOFTWARE	HIS A:149 , LYS A:382 , SO4 A:501 , HOH A:817 , HOH A:986 , HOH A:1210 , HOH A:1213	BINDING SITE FOR RESIDUE EDO A 803
10	BC1	SOFTWARE	SER A:204 , ARG A:207 , ARG A:208 , TYR A:244 , LYS A:248 , ARG A:327 , HOH A:1079 , HOH A:1148 , HOH A:1242	BINDING SITE FOR RESIDUE GOL A 804

(no "SS Bond" information available for 2QB6)

Asymmetric Unit

No.	Residues
1	Glu A:159	-	Pro A:160
2	Glu B:159	-	Pro B:160

(no "SAP(SNP)/Variant" information available for 2QB6)

(no "PROSITE Motif" information available for 2QB6)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YHR201C	1	YHR201C.1	VIII:501143-499950	1194	PPX1_YEAST	1-397	397	2	A:5-397 B:4-397 (gaps)	393 394

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:393
 aligned with PPX1_YEAST | P38698 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:393
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394   
           PPX1_YEAST     5 RKTVPEFLAHLKSLPISKIASNDVLTICVGNESADMDSIASAITYSYCQYIYNEGTYSEEKKKGSFIVPIIDIPREDLSLRRDVMYVLEKLKIKEEELFFIEDLKSLKQNVSQGTELNSYLVDNNDTPKNLKNYIDNVVGIIDHHFDLQKHLDAEPRIVKVSGSCSSLVFNYWYEKLQGDREVVMNIAPLLMGAILIDTSNMRRKVEESDKLAIERCQAVLSGAVNEVSAQGLEDSSEFYKEIKSRKNDIKGFSVSDILKKDYKQFNFQGKGHKGLEIGLSSIVKRMSWLFNEHGGEADFVNQCRRFQAERGLDVLVLLTSWRKAGDSHRELVILGDSNVVRELIERVSDKLQLQLFGGNLDGGVAMFKQLNVEATRKQVVPYLEEAYSNLEE 397
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh............eee...hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh....eeeeeee.....hhhhh....eeeeeee.............eee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhh.eeeeee.......eeeeeeee..hhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhheeeeeeehhh.eeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-397 UniProt: 1-397 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 2qb6 A   5 RKTVPEFLAHLKSLPISKIASNDVLTICVGNESADMDSIASAITYSYCQYIYNEGTYSEEKKKGSFIVPIIDIPREDLSLRRDVMYVLEKLKIKEEELFFIEDLKSLKQNVSQGTELNSYLVDNNDTPKNLKNYIDNVVGIIDHHFDLQKHLDAEPRIVKVSGSCSSLVFNYWYEKLQGDREVVMNIAPLLMGAILIDTSNMRRKVEESDKLAIERCQAVLSGAVNEVSAQGLEDSSEFYKEIKSRKNDIKGFSVSDILKKDYKQFNFQGKGHKGLEIGLSSIVKRMSWLFNEHGGEADFVNQCRRFQAERGLDVLVLLTSWRKAGDSHRELVILGDSNVVRELIERVSDKLQLQLFGGNLDGGVAMFKQLNVEATRKQVVPYLEEAYSNLEE 397
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394

Chain B from PDB  Type:PROTEIN  Length:388
 aligned with PPX1_YEAST | P38698 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:394
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    
           PPX1_YEAST     4 LRKTVPEFLAHLKSLPISKIASNDVLTICVGNESADMDSIASAITYSYCQYIYNEGTYSEEKKKGSFIVPIIDIPREDLSLRRDVMYVLEKLKIKEEELFFIEDLKSLKQNVSQGTELNSYLVDNNDTPKNLKNYIDNVVGIIDHHFDLQKHLDAEPRIVKVSGSCSSLVFNYWYEKLQGDREVVMNIAPLLMGAILIDTSNMRRKVEESDKLAIERCQAVLSGAVNEVSAQGLEDSSEFYKEIKSRKNDIKGFSVSDILKKDYKQFNFQGKGHKGLEIGLSSIVKRMSWLFNEHGGEADFVNQCRRFQAERGLDVLVLLTSWRKAGDSHRELVILGDSNVVRELIERVSDKLQLQLFGGNLDGGVAMFKQLNVEATRKQVVPYLEEAYSNLEE 397
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------DHH-2qb6B03 B:24-200                                                                                                                                                             -------------------------------------------DHHA2-2qb6B01 B:244-392                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) --------------------DHH-2qb6B04 B:24-200                                                                                                                                                             -------------------------------------------DHHA2-2qb6B02 B:244-392                                                                                                                              ----- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhh............eeee...hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh....eeeeeee.....hhhhh....eeeeeee.............eee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhhh.eeeee.------..eeeeeee..hhhhhhhhh.hhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhheeeeeee....eeeeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-397 (gaps) UniProt: 1-397 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 2qb6 B   4 LRKTVPEFLAHLKSLPISKIASNDVLTICVGNESADMDSIASAITYSYCQYIYNEGTYSEEKKKGSFIVPIIDIPREDLSLRRDVMYVLEKLKIKEEELFFIEDLKSLKQNVSQGTELNSYLVDNNDTPKNLKNYIDNVVGIIDHHFDLQKHLDAEPRIVKVSGSCSSLVFNYWYEKLQGDREVVMNIAPLLMGAILIDTSNMRRKVEESDKLAIERCQAVLSGAVNEVSAQGLEDSSEFYKEIKSRKNDIKGFSVSDILKKDYKQFNF------GLEIGLSSIVKRMSWLFNEHGGEADFVNQCRRFQAERGLDVLVLLTSWRKAGDSHRELVILGDSNVVRELIERVSDKLQLQLFGGNLDGGVAMFKQLNVEATRKQVVPYLEEAYSNLEE 397
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263        |-     | 283       293       303       313       323       333       343       353       363       373       383       393    
                                                                                                                                                                                                                                                                                                      272    279

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 2QB6)

(no "CATH Domain" information available for 2QB6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPX1_YEAST | P38698)

molecular function
	GO:0004309	exopolyphosphatase activity	Catalysis of the reaction: polyphosphate(n) + H2O = polyphosphate(n-1) + 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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016462	pyrophosphatase activity	Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.
biological process
	GO:0006798	polyphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a polyphosphate, the anion or salt of polyphosphoric acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:159 - Pro A:160	[ RasMol ]
		Glu B:159 - Pro B:160	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	2qb6
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	PPX1_YEAST \| P38698
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	3.6.1.11
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UniProtKB/Swiss-Prot
	PPX1_YEAST \| P38698	:	2qb7 2qb8

2qb7	SACCHAROMYCES CEREVISIAE CYTOSOLIC EXOPOLYPHOSPHATASE, PHOSPHATE COMPLEX
2qb8	SACCHAROMYCES CEREVISIAE CYTOSOLIC EXOPOLYPHOSPHATASE, ATP COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

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