1DK4 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MJ0109 GENE PRODUCT INOSITOL MONOPHOSPHATASE

Authors :   B. Stec, H. Yang, K. A. Johnson, L. Chen, M. F. Roberts

Date :   06 Dec 99 (Deposition) - 08 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Homodimer, Complexed With Zn And Pi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Stec, H. Yang, K. A. Johnson, L. Chen, M. F. Roberts
Mj0109 Is An Enzyme That Is Both An Inositol Monophosphatase And The 'Missing' Archaeal Fructose-1, 6-Bisphosphatase.
Nat. Struct. Biol. V. 7 1046 2000
PubMed-ID: 11062561 | Reference-DOI: 10.1038/80968
(for further references see the PDB file header)

Molecule 1 - INOSITOL MONOPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23A(+)
	Expression System Taxid	:	562
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION
2	ZN	6	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:65 , ASP A:81 , ASP A:84 , ASP A:201 , ZN A:291 , PO4 A:293	BINDING SITE FOR RESIDUE ZN A 290
2	AC2	SOFTWARE	GLU A:65 , ASP A:81 , ILE A:83 , ZN A:290 , PO4 A:293 , HOH A:633	BINDING SITE FOR RESIDUE ZN A 291
3	AC3	SOFTWARE	GLU A:65 , PO4 A:293 , HOH A:632	BINDING SITE FOR RESIDUE ZN A 292
4	AC4	SOFTWARE	GLU A:65 , ASP A:81 , ILE A:83 , ASP A:84 , GLY A:85 , SER A:86 , ARG A:198 , ASP A:201 , ZN A:290 , ZN A:291 , ZN A:292 , HOH A:632	BINDING SITE FOR RESIDUE PO4 A 293
5	AC5	SOFTWARE	GLU B:365 , ASP B:381 , ILE B:383 , ZN B:591 , PO4 B:593 , HOH B:609	BINDING SITE FOR RESIDUE ZN B 590
6	AC6	SOFTWARE	ASP B:381 , ASP B:384 , ASP B:501 , ZN B:590 , PO4 B:593 , HOH B:629	BINDING SITE FOR RESIDUE ZN B 591
7	AC7	SOFTWARE	ASP B:338 , GLU B:365 , ARG B:498 , PO4 B:593 , HOH B:620	BINDING SITE FOR RESIDUE ZN B 592
8	AC8	SOFTWARE	ASP B:338 , GLU B:365 , ASP B:381 , ILE B:383 , ASP B:384 , GLY B:385 , SER B:386 , ARG B:498 , ASP B:501 , ZN B:590 , ZN B:591 , ZN B:592 , HOH B:629	BINDING SITE FOR RESIDUE PO4 B 593

(no "SS Bond" information available for 1DK4)

(no "Cis Peptide Bond" information available for 1DK4)

(no "SAP(SNP)/Variant" information available for 1DK4)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IMP_1	PS00629	Inositol monophosphatase family signature 1.	BSUHB_METJA	78-91	2	A:78-91 B:378-391
2	IMP_2	PS00630	Inositol monophosphatase family signature 2.	BSUHB_METJA	200-214	2	A:200-214 B:500-514

(no "Exon" information available for 1DK4)

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:252
 aligned with BSUHB_METJA | Q57573 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    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  
          BSUHB_METJA     1 MKWDEIGKNIAKEIEKEILPYFGRKDKSYVVGTSPSGDETEIFDKISEDIALKYLKSLNVNIVSEELGVIDNSSEWTVVIDPIDGSFNFINGIPFFAFCFGVFKNNEPYYGLTYEFLTKSFYEAYKGKGAYLNGRKIKVKDFNPNNIVISYYPSKKIDLEKLRNKVKRVRIFGAFGLEMCYVAKGTLDAVFDVRPKVRAVDIASSYIICKEAGALITDENGDELKFDLNATDRLNIIVANSKEMLDIILDLL 252
               SCOP domains d1dk4a_ A: Archaeal inositol monophosphatase/fructose-1,6-bisphosphatase                                                                                                                                                                                     SCOP domains
               CATH domains 1dk4A01 A:1-137 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                         1dk4A02 A:138-252  [code=3.40.190.80, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..........eeee.....eeehhhhhhhhhhhhhhh....eeee...eee.....eeeeee...hhhhhhh......eeeeeee...eeeeeeee....eeeeee...eeee..ee......hhhhh.ee.......hhhhhhhhh.......hhhhhhhhhhh....eee......hhhhhhhhhhhhhh.........................eee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------IMP_1         ------------------------------------------------------------------------------------------------------------IMP_2          -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dk4 A   1 MKWDEIGKNIAKEIEKEILPYFGRKDKSYVVGTSPSGDETEIFDKISEDIALKYLKSLNVNIVSEELGVIDNSSEWTVVIDPIDGSFNFINGIPFFAFCFGVFKNNEPYYGLTYEFLTKSFYEAYKGKGAYLNGRKIKVKDFNPNNIVISYYPSKKIDLEKLRNKVKRVRIFGAFGLEMCYVAKGTLDAVFDVRPKVRAVDIASSYIICKEAGALITDENGDELKFDLNATDRLNIIVANSKEMLDIILDLL 252
                                    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

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with BSUHB_METJA | Q57573 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    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  
          BSUHB_METJA     1 MKWDEIGKNIAKEIEKEILPYFGRKDKSYVVGTSPSGDETEIFDKISEDIALKYLKSLNVNIVSEELGVIDNSSEWTVVIDPIDGSFNFINGIPFFAFCFGVFKNNEPYYGLTYEFLTKSFYEAYKGKGAYLNGRKIKVKDFNPNNIVISYYPSKKIDLEKLRNKVKRVRIFGAFGLEMCYVAKGTLDAVFDVRPKVRAVDIASSYIICKEAGALITDENGDELKFDLNATDRLNIIVANSKEMLDIILDLL 252
               SCOP domains d1dk4b_ B: Archaeal inositol monophosphatase/fructose-1,6-bisphosphatase                                                                                                                                                                                     SCOP domains
               CATH domains 1dk4B01 B:301-437 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                       1dk4B02 B:438-552  [code=3.40.190.80, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhh.eeee.....eeehhhhhhhhhhhhhhh....eeee...eee.....eeeeee...hhhhhhh......eeeeeee...eeeeeeee....eeeeee...eeee..ee............eeee.....hhhhhhh.........hhhhhhhhhhh....eeee.....hhhhhhhhhhhhhh...ee...................eeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------IMP_1         ------------------------------------------------------------------------------------------------------------IMP_2          -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dk4 B 301 MKWDEIGKNIAKEIEKEILPYFGRKDKSYVVGTSPSGDETEIFDKISEDIALKYLKSLNVNIVSEELGVIDNSSEWTVVIDPIDGSFNFINGIPFFAFCFGVFKNNEPYYGLTYEFLTKSFYEAYKGKGAYLNGRKIKVKDFNPNNIVISYYPSKKIDLEKLRNKVKRVRIFGAFGLEMCYVAKGTLDAVFDVRPKVRAVDIASSYIICKEAGALITDENGDELKFDLNATDRLNIIVANSKEMLDIILDLL 552
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550

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 1DK4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BSUHB_METJA | Q57573)

molecular function
	GO:0042132	fructose 1,6-bisphosphate 1-phosphatase activity	Catalysis of the reaction: D-fructose 1,6-bisphosphate + H2O = D-fructose 6-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:0008934	inositol monophosphate 1-phosphatase activity	Catalysis of the reaction: myo-inositol 1-phosphate + H2O = myo-inositol + phosphate.
	GO:0052832	inositol monophosphate 3-phosphatase activity	Catalysis of the reaction: myo-inositol 3-phosphate + H2O = myo-inositol + phosphate.
	GO:0052833	inositol monophosphate 4-phosphatase activity	Catalysis of the reaction: myo-inositol 4-phosphate + H2O = myo-inositol + phosphate.
	GO:0052834	inositol monophosphate phosphatase activity	Catalysis of the reaction: myo-inositol phosphate + H2O = myo-inositol + 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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	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.
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
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1dk4)

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
	1dk4
		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
	BSUHB_METJA \| Q57573
		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)
	3.1.3.25
		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
	BSUHB_METJA \| Q57573
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BSUHB_METJA \| Q57573	:	1g0h 1g0i

1awb	HUMAN INOSITOL MONOPHOSPHATASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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