1NV1 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FRUCTOSE-1,6-BISPHOSPHATASE COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND THALLIUM (5 MM)

Authors :   J. Choe, C. V. Iancu, H. J. Fromm, R. B. Honzatko

Date :   01 Feb 03 (Deposition) - 08 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (4x)

Keywords :   Bisphosphatase, Allosteric Enzymes, Gluconeogenesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Y. Choe, S. W. Nelson, H. J. Fromm, R. B. Honzatko
Interaction Of Tl+ With Product Complexes Of Fructose-1, 6-Bisphosphatase
J. Biol. Chem. V. 278 16008 2003
PubMed-ID: 12595529 | Reference-DOI: 10.1074/JBC.M212394200

Molecule 1 - FRUCTOSE-1,6-BISPHOSPHATASE
	Chains	:	A
	EC Number	:	3.1.3.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	F6P	1	Ligand/Ion	FRUCTOSE-6-PHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	TL	6	Ligand/Ion	THALLIUM (I) ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	F6P	1	Ligand/Ion	FRUCTOSE-6-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	TL	-1	Ligand/Ion	THALLIUM (I) ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	F6P	4	Ligand/Ion	FRUCTOSE-6-PHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PO4	8	Ligand/Ion	PHOSPHATE ION
4	TL	-1	Ligand/Ion	THALLIUM (I) ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:1121 , GLY A:1122 , ASN A:1212 , TYR A:1215 , ARG A:1243 , TYR A:1244 , GLY A:1246 , MET A:1248 , TYR A:1264 , LYS A:1274 , GLU A:1280 , PO4 A:2340 , MG A:2341 , TL A:2342 , TL A:2348 , HOH A:3001 , HOH A:3026 , HOH A:3036 , HOH A:3039 , HOH A:3053 , HOH A:3108	BINDING SITE FOR RESIDUE F6P A 2339
02	AC2	SOFTWARE	ASP A:1118 , ASP A:1121 , GLU A:1280 , F6P A:2339 , PO4 A:2340 , TL A:2344	BINDING SITE FOR RESIDUE MG A 2341
03	AC3	SOFTWARE	GLU A:1097 , GLU A:1098 , ASP A:1118 , LEU A:1120 , PO4 A:2340 , TL A:2346	BINDING SITE FOR RESIDUE MG A 2343
04	AC4	SOFTWARE	GLY A:1026 , THR A:1027 , GLY A:1028 , GLU A:1029 , MET A:1030 , LYS A:1112 , TYR A:1113 , HOH A:3087	BINDING SITE FOR RESIDUE PO4 A 2338
05	AC5	SOFTWARE	ASP A:1068 , GLU A:1097 , ASP A:1118 , LEU A:1120 , ASP A:1121 , GLY A:1122 , SER A:1123 , GLU A:1280 , F6P A:2339 , MG A:2341 , TL A:2342 , MG A:2343 , TL A:2344 , TL A:2345 , TL A:2346 , TL A:2347	BINDING SITE FOR RESIDUE PO4 A 2340
06	AC6	SOFTWARE	ASP A:1118 , ASP A:1121 , GLU A:1280 , F6P A:2339 , PO4 A:2340	BINDING SITE FOR RESIDUE TL A 2342
07	AC7	SOFTWARE	GLU A:1097 , ASP A:1118 , LEU A:1120 , PO4 A:2340 , MG A:2341	BINDING SITE FOR RESIDUE TL A 2344
08	AC8	SOFTWARE	ASN A:1064 , ASP A:1068 , ASP A:1074 , GLU A:1097 , GLU A:1098 , PO4 A:2340	BINDING SITE FOR RESIDUE TL A 2345
09	AC9	SOFTWARE	ASP A:1074 , LEU A:1120 , SER A:1123 , PO4 A:2340 , MG A:2343	BINDING SITE FOR RESIDUE TL A 2346
10	BC1	SOFTWARE	GLU A:1097 , ARG A:1276 , PO4 A:2340 , TL A:2348	BINDING SITE FOR RESIDUE TL A 2347
11	BC2	SOFTWARE	LYS A:1274 , GLU A:1280 , F6P A:2339 , TL A:2347	BINDING SITE FOR RESIDUE TL A 2348

(no "SS Bond" information available for 1NV1)

(no "Cis Peptide Bond" information available for 1NV1)

(no "SAP(SNP)/Variant" information available for 1NV1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FBPASE	PS00124	Fructose-1-6-bisphosphatase active site.	F16P1_PIG	274-286	1	A:1273-1285

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FBPASE	PS00124	Fructose-1-6-bisphosphatase active site.	F16P1_PIG	274-286	1	A:1273-1285

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FBPASE	PS00124	Fructose-1-6-bisphosphatase active site.	F16P1_PIG	274-286	4	A:1273-1285

(no "Exon" information available for 1NV1)

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:331
 aligned with F16P1_PIG | P00636 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:331
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 
           F16P1_PIG      8 DTNIVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK  338
               SCOP domains d1nv1a_ A: Fructose-1,6-bisphosphatase                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --1nv1A01 A:1009-1199 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                                                                                                           1nv1A02 A:1200-1334  [code=3.40.190.80, no name defined]                                                                               --- CATH domains
               Pfam domains ----FBPase-1nv1A01 A:1011-1334                                                                                                                                                                                                                                                                                                          --- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........eeeee.....eeehhhhhhhhhhhhhhhhh..eeeeee......ee.hhh.eeeeeeeeeeeehhhhh.....eeeeeeeee.......hhhhhh.hhhhh.eeeeeee...eeeeeee..eeeeeeee....eeeeee..........eee.hhhhhhhhhhhhhhhhhhhhh........ee....hhhhhhhhhhhhh.eeee...............hhhhhhhhhhhh..eee....hhhhh..........eeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FBPASE       ---------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nv1 A 1007 DTNIVTLTRFVMEEGRKARGTGEMTQLLNSLCTAVKAISTAVRKAGIAHLYGIAGSTNVTGDQVKKLDVLSNDLVINVLKSSFATCVLVSEEDKNAIIVEPEKRGKYVVCFDPLDGSSNIDCLVSIGTIFGIYRKNSTDEPSEKDALQPGRNLVAAGYALYGSATMLVLAMVNGVNCFMLDPAIGEFILVDRDVKIKKKGSIYSINEGYAKEFDPAITEYIQRKKFPPDNSAPYGARYVGSMVADVHRTLVYGGIFMYPANKKSPKGKLRLLYECNPMAYVMEKAGGLATTGKEAVLDIVPTDIHQRAPIILGSPEDVTELLEIYQKHAAK 1337
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Carbohydrate phosphatase (140)

Superfamily: Carbohydrate phosphatase (140)

Family: Inositol monophosphatase/fructose-1,6-bisphosphatase-like (121)

Protein domain: Fructose-1,6-bisphosphatase (75)

Pig (Sus scrofa) [TaxId: 9823] (65)

d1nv1a_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Fructose-1,6-Bisphosphatase; Chain A, domain 1 (114)

Homologous Superfamily: Fructose-1,6-Bisphosphatase, subunit A, domain 1 (114)

Pig (Sus scrofa) (54)

1nv1A01

A:1009-1199

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: [code=3.40.190.80, no name defined] (109)

Pig (Sus scrofa) (54)

1nv1A02

A:1200-1334

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phospoesterase (42)

Family: FBPase (32)

Sus scrofa (Pig) (19)

FBPase-1nv1A01

A:1011-1334

Asymmetric Unit(hide GO term definitions)

Chain A (F16P1_PIG | P00636)

molecular function
	GO:0016208	AMP binding	Interacting selectively and non-covalently with AMP, adenosine monophosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0048029	monosaccharide binding	Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
	GO:0042578	phosphoric ester hydrolase activity	Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
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:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0071286	cellular response to magnesium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a magnesium ion stimulus.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006002	fructose 6-phosphate metabolic process	The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0046580	negative regulation of Ras protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0045820	negative regulation of glycolytic process	Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0006111	regulation of gluconeogenesis	Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nv1)

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	1nv1
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	3.1.3.11
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1nuz	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE AND PHOSPHATE, AT 1.9A
1nv0	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 1MM THALLIUM
1nv2	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 20MM THALLIUM
1nv3	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 100MM THALLIUM
1nv4	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE, EDTA AND 1MM THALLIUM
1nv5	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE, EDTA AND 5MM THALLIUM
1nv6	COMPLEX WITH MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE, EDTA AND 20MM THALLIUM
1nv7	COMPLEX WITH AMP, MAGNESIUM, FRUCTOSE-6-PHOSPHATE, PHOSPHATE AND 20MM THALLIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (21, 21)

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Related Entries Specified in the PDB File