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Title :   STRUCTURE OF THE FAMILY II INORGANIC PYROPHOSPHATASE FROM STREPTOCOCCUS AGALACTIAE AT 2.8 RESOLUTION

Authors :   M. K. Rantanen, L. Lehtio, L. Rajagopal, C. E. Rubens, A. Goldman

Date :   28 Mar 07 (Deposition) - 29 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Streptococcus Agalactiae, Family Ii, Inorganic, Pyrophosphatase, Signalling, Phosphorylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Rantanen, L. Lehtio, L. Rajagopal, C. E. Rubens, A. Goldman
Structure Of The Streptococcus Agalactiae Family Ii Inorganic Pyrophosphatase At 2. 80 A Resolution
Acta Crystallogr. , Sect. D V. 63 738 2007
PubMed-ID: 17505113 | Reference-DOI: 10.1107/S0907444907019695

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX4T3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PPAC
	Organism Scientific	:	STREPTOCOCCUS AGALACTIAE
	Organism Taxid	:	205921
	Strain	:	A909
	Synonym	:	FAMILY II INORGANIC PYROPHOSPHATASE, IMIDODIPHOSPHATE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	2PN	2	Ligand/Ion	IMIDODIPHOSPHORIC ACID
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MN	4	Ligand/Ion	MANGANESE (II) ION
4	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	2PN	2	Ligand/Ion	IMIDODIPHOSPHORIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	2PN	2	Ligand/Ion	IMIDODIPHOSPHORIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	TRP	2	Mod. Amino Acid	TRYPTOPHAN

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:9 , ASP A:13 , ASP A:77 , MN A:402 , 2PN A:1001	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	ASP A:15 , ASP A:77 , HIS A:99 , ASP A:151 , MN A:401 , 2PN A:1001	BINDING SITE FOR RESIDUE MN A 402
03	AC3	SOFTWARE	ARG A:297 , 2PN A:1001 , HOH A:1099	BINDING SITE FOR RESIDUE MG A 501
04	AC4	SOFTWARE	HIS A:9 , ASP A:77 , HIS A:99 , HIS A:100 , ASP A:151 , LYS A:207 , ARG A:297 , LYS A:298 , MN A:401 , MN A:402 , MG A:501 , HOH A:1085 , HOH A:1099	BINDING SITE FOR RESIDUE 2PN A 1001
05	AC5	SOFTWARE	TRP A:31 , TYR A:94 , GLY A:95 , VAL A:97 , TYR A:112	BINDING SITE FOR RESIDUE TRP A 1031
06	AC6	SOFTWARE	HIS B:9 , ASP B:13 , ASP B:77 , MN B:404 , 2PN B:1002	BINDING SITE FOR RESIDUE MN B 403
07	AC7	SOFTWARE	ASP B:15 , ASP B:77 , HIS B:99 , ASP B:151 , MN B:403 , 2PN B:1002	BINDING SITE FOR RESIDUE MN B 404
08	AC8	SOFTWARE	2PN B:1002	BINDING SITE FOR RESIDUE MG B 502
09	AC9	SOFTWARE	HIS B:9 , ASP B:13 , ASP B:77 , HIS B:99 , HIS B:100 , ASP B:151 , LYS B:207 , ARG B:297 , LYS B:298 , MN B:403 , MN B:404 , MG B:502 , HOH B:2097	BINDING SITE FOR RESIDUE 2PN B 1002
10	BC1	SOFTWARE	TRP B:31 , TYR B:94 , TYR B:112 , MET B:128 , HOH B:2060	BINDING SITE FOR RESIDUE TRP B 2031

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

(no "Cis Peptide Bond" information available for 2ENX)

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

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

(no "Exon" information available for 2ENX)

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:310
 aligned with PPAC_STRA1 | Q3K0B5 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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
           PPAC_STRA1     2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
               SCOP domains d2enxa_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2enxA01 A:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh.........hhhhhh..eeeee...hhhhh.......eeeeeee.............eeee.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2enx A   2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
                                    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

Chain A from PDB  Type:PROTEIN  Length:310
 aligned with PPAC_STRA5 | Q8DYS6 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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
           PPAC_STRA5     2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
               SCOP domains d2enxa_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2enxA01 A:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh.........hhhhhh..eeeee...hhhhh.......eeeeeee.............eeee.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeee.hhhhhhhhhh......eeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2enx A   2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
                                    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

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with PPAC_STRA1 | Q3K0B5 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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
           PPAC_STRA1     2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
               SCOP domains d2enxb_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2enxB01 B:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhh.................eeeee..........hhhhheeeeeee.............eeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhh.eeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeee..hhhhhhhhhh......eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2enx B   2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
                                    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

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with PPAC_STRA5 | Q8DYS6 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:310
                                    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
           PPAC_STRA5     2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
               SCOP domains d2enxb_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2enxB01 B:2-191 inorganic pyrophosphatase (n-terminal core)                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhh.................eeeee..........hhhhheeeeeee.............eeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhh.eeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeee..hhhhhhhhhh......eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2enx B   2 SKILVFGHQNPDSDAIGSSVAFAYLAKEAWGLDTEAVALGTPNEETAYVLDYFGVQAPRVVESAKAEGVETVILTDHNEFQQSISDIKDVTVYGVVDHHRVANFETANPLYMRLEPVGSASSIVYRMFKENGVSVPKELAGLLLSGLISDTLLLKSPTTHASDIPVAKELAELAGVNLEEYGLEMLKAGTNLSSKTAAELIDIDAKTFELNGEAVRVAQVNTVDINDILARQEEIEVAIQEAIVTEGYSDFVLMITDIVNSNSEILALGSNMAKVEAAFEFTLENNHAFLAGAVSRKKQVVPQLTESYNA 311
                                    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

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: DHH phosphoesterases (11)

Superfamily: DHH phosphoesterases (11)

Family: Manganese-dependent inorganic pyrophosphatase (family II) (9)

Protein domain: automated matches (1)

Streptococcus agalactiae [TaxId: 205921] (1)

1a	d2enxa_	A:
1b	d2enxb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: inorganic pyrophosphatase (n-terminal core) (10)

Homologous Superfamily: inorganic pyrophosphatase (n-terminal core) (10)

Streptococcus agalactiae a909. Organism_taxid: 205921. Strain: a909. (1)

1a	2enxA01	A:2-191
1b	2enxB01	B:2-191

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPAC_STRA1 | Q3K0B5)

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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B (PPAC_STRA5 | Q8DYS6)

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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Description

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

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