2IW4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF BASILLUS SUBTILIS FAMILY II INORGANIC PYROPHOSPHATASE MUTANT, H98Q, IN COMPLEX WITH PNP

Authors :   I. P. Fabrichniy, L. Lehtio, E. Oksanen, A. Goldman

Date :   26 Jun 06 (Deposition) - 07 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Hydrolase, Pyrophosphatase, Substrate Complex, Mutant, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. P. Fabrichniy, L. Lehtio, M. Tammenkoski, A. B. Zyryanov, E. Oksanen, A. A. Baykov, R. Lahti, A. Goldman
A Trimetal Site And Substrate Distortion In A Family Ii Inorganic Pyrophosphatase.
J. Biol. Chem. V. 282 1422 2007
PubMed-ID: 17095506 | Reference-DOI: 10.1074/JBC.M513161200

Molecule 1 - MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	C43 (DE3)
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	INORGANIC PYROPHOSPHATASE, PYROPHOSPHATE PHOSPHO-HYDROLASE, PPASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 19)

No.	Name	Count	Type	Full Name
1	2PN	2	Ligand/Ion	IMIDODIPHOSPHORIC ACID
2	FE	4	Ligand/Ion	FE (III) ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	MG	4	Ligand/Ion	MAGNESIUM ION
5	MN	3	Ligand/Ion	MANGANESE (II) ION
6	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
7	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:9 , ASP A:13 , ASP A:75 , FE A:1310 , MG A:1312 , MN A:1314 , 2PN A:1315 , HOH A:2195	BINDING SITE FOR RESIDUE FE A1309
02	AC2	SOFTWARE	ASP A:15 , ASP A:75 , HIS A:97 , ASP A:149 , FE A:1309 , MN A:1313 , 2PN A:1315 , HOH A:2195	BINDING SITE FOR RESIDUE FE A1310
03	AC3	SOFTWARE	MG A:1312 , 2PN A:1315 , HOH A:2013 , HOH A:2131 , HOH A:2198 , HOH A:2199	BINDING SITE FOR RESIDUE MG A1311
04	AC4	SOFTWARE	ASP A:13 , ASP A:149 , FE A:1309 , MG A:1311 , MN A:1313 , 2PN A:1315 , HOH A:2105 , HOH A:2195 , HOH A:2199	BINDING SITE FOR RESIDUE MG A1312
05	AC5	SOFTWARE	HIS A:9 , ASP A:13 , ASP A:75 , FE A:1310 , MG A:1312 , MN A:1314 , 2PN A:1315 , HOH A:2195	BINDING SITE FOR RESIDUE MN A1313
06	AC6	SOFTWARE	ASP A:15 , ASP A:75 , HIS A:97 , ASP A:149 , FE A:1309 , MN A:1313 , 2PN A:1315 , HOH A:2195	BINDING SITE FOR RESIDUE MN A1314
07	AC7	SOFTWARE	ARG A:38 , GLN A:41	BINDING SITE FOR RESIDUE SO4 A1316
08	AC8	SOFTWARE	HIS B:9 , ASP B:13 , ASP B:75 , FE B:1312 , MG B:1314 , MN B:1317 , 2PN B:1318 , HOH B:2283	BINDING SITE FOR RESIDUE FE B1311
09	AC9	SOFTWARE	ASP B:15 , ASP B:75 , HIS B:97 , ASP B:149 , FE B:1311 , 2PN B:1318 , HOH B:2283	BINDING SITE FOR RESIDUE FE B1312
10	BC1	SOFTWARE	MG B:1314 , 2PN B:1318 , HOH B:2023 , HOH B:2219 , HOH B:2285 , HOH B:2286	BINDING SITE FOR RESIDUE MG B1313
11	BC2	SOFTWARE	ASP B:13 , ASP B:149 , FE B:1311 , MG B:1313 , 2PN B:1318 , HOH B:2187 , HOH B:2283 , HOH B:2285	BINDING SITE FOR RESIDUE MG B1314
12	BC3	SOFTWARE	ASP B:15 , ASP B:75 , HIS B:97 , ASP B:149 , FE B:1311 , 2PN B:1318 , HOH B:2283	BINDING SITE FOR RESIDUE MN B1317
13	BC4	SOFTWARE	ARG B:38 , GLN B:41 , HOH B:2287	BINDING SITE FOR RESIDUE SO4 B1319
14	BC5	SOFTWARE	HIS A:9 , ASP A:13 , ASP A:75 , HIS A:97 , GLN A:98 , ASP A:149 , LYS A:205 , ARG A:295 , LYS A:296 , FE A:1309 , FE A:1310 , MG A:1311 , MG A:1312 , MN A:1313 , MN A:1314 , HOH A:2013 , HOH A:2131 , HOH A:2146 , HOH A:2187 , HOH A:2195 , HOH A:2196 , HOH A:2197 , HOH A:2198 , HOH A:2199	BINDING SITE FOR RESIDUE 2PN A1315
15	BC6	SOFTWARE	TYR B:23 , LYS B:27 , LEU B:30 , PHE B:32 , GLU B:93 , TYR B:110 , ASN B:130 , HOH B:2135	BINDING SITE FOR RESIDUE PG4 B1309
16	BC7	SOFTWARE	MET B:1 , GLU B:2 , LYS B:128 , LYS B:167 , GLU B:168 , GLU B:171 , HOH B:2199	BINDING SITE FOR RESIDUE PG4 B1310
17	BC8	SOFTWARE	HIS B:9 , ASP B:13 , ASP B:75 , HIS B:97 , GLN B:98 , ASP B:149 , LYS B:205 , ARG B:295 , LYS B:296 , FE B:1311 , FE B:1312 , MG B:1313 , MG B:1314 , MN B:1317 , HOH B:2023 , HOH B:2137 , HOH B:2219 , HOH B:2234 , HOH B:2275 , HOH B:2283 , HOH B:2284 , HOH B:2285 , HOH B:2286	BINDING SITE FOR RESIDUE 2PN B1318
18	BC9	SOFTWARE	ASN B:69 , LYS B:133 , GLU B:135 , LYS B:136 , HOH B:2180 , HOH B:2282	BINDING SITE FOR RESIDUE GOL B1315
19	CC1	SOFTWARE	THR B:195 , VAL B:196 , GLU B:197 , ARG B:230 , GLU B:233	BINDING SITE FOR RESIDUE GOL B1316

(no "SS Bond" information available for 2IW4)

(no "Cis Peptide Bond" information available for 2IW4)

(no "SAP(SNP)/Variant" information available for 2IW4)

(no "PROSITE Motif" information available for 2IW4)

(no "Exon" information available for 2IW4)

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:308
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    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        
           PPAC_BACSU     2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
               SCOP domains d2iw4a_ A: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2iw4A01 A:2-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                 ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhhhhhh......eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iw4 A   2 EKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHQRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
                                    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

Chain B from PDB  Type:PROTEIN  Length:309
 aligned with PPAC_BACSU | P37487 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:309
                                    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       290       300         
           PPAC_BACSU     1 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHHRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
               SCOP domains d2iw4b_ B: Manganese-dependent inorganic pyrophosphatase (family II)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2iw4B01 B:1-189 inorganic pyrophosphatase (n-terminal core)                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.....ee.........eeeee...hhhhh..hhhhheeeeeee.............eeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhh...eeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhhhhhh......eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iw4 B   1 MEKILIFGHQNPDTDTICSAIAYADLKNKLGFNAEPVRLGQVNGETQYALDYFKQESPRLVETAANEVNGVILVDHNERQQSIKDIEEVQVLEVIDHQRIANFETAEPLYYRAEPVGCTATILNKMYKENNVKIEKEIAGLMLSAIISDSLLFKSPTCTDQDVAAAKELAEIAGVDAEEYGLNMLKAGADLSKKTVEELISLDAKEFTLGSKKVEIAQVNTVDIEDVKKRQAELEAVISKVVAEKNLDLFLLVITDILENDSLALAIGNEAAKVEKAFNVTLENNTALLKGVVSRKKQVVPVLTDAMAE 309
                                    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       290       300

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: 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: Manganese-dependent inorganic pyrophosphatase (family II) (8)

Bacillus subtilis [TaxId: 1423] (5)

1a	d2iw4a_	A:
1b	d2iw4b_	B:

Asymmetric/Biological 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)

Bacillus subtilis. Organism_taxid: 1423. (5)

1a	2iw4A01	A:2-189
1b	2iw4B01	B:1-189

(no "Pfam Domain" information available for 2IW4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PPAC_BACSU | P37487)

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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		2PN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2iw4)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2iw4
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PPAC_BACSU \| P37487
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.6.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PPAC_BACSU \| P37487
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PPAC_BACSU \| P37487	:	1k23 1wpm 1wpn 2haw

1k23	INORGANIC PYROPHOSPHATASE (FAMILY II) FROM BACILLUS SUBTILIS
1wpm	STRUCTURE OF BACILLUS SUBTILIS INORGANIC PYROPHOSPHATASE
1wpn	CRYSTAL STRUCTURE OF THE N-TERMINAL CORE OF BACILLUSSUBTILIS INORGANIC PYROPHOSPHATASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File