3BIF - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE EMPTY 6-PF-2K ACTIVE SITE

Authors :   M. H. Yuen, C. A. Hasemann

Date :   05 May 99 (Deposition) - 29 Sep 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Kinase, Phosphotransferase, Phosphatase, Hydrolase (Phospho), Glycolysis, Bifunctional Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Yuen, X. L. Wang, H. Mizuguchi, K. Uyeda, C. A. Hasemann
A Switch In The Kinase Domain Of Rat Testis 6-Phosphofructo-2-Kinase/Fructose-2, 6- Bisphosphatase.
Biochemistry V. 38 12333 1999
PubMed-ID: 10493801 | Reference-DOI: 10.1021/BI991268+
(for further references see the PDB file header)

Molecule 1 - PROTEIN (6-PHOSPHOFRUCTO-2-KINASE/ FRUCTOSE-2,6- BISPHOSPHATASE)
	Cell Line	:	BL21
	Chains	:	A
	EC Number	:	2.7.1.105
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21
	Expression System Gene	:	RT2K
	Expression System Plasmid	:	PT7-7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RT2K
	Mutation	:	YES
	Organ	:	TESTIS
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	BIFUNCTIONAL ENZYME, ALSO EC 3.1.3.46

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	SIN	1	Ligand/Ion	SUCCINIC ACID

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	BOG	4	Ligand/Ion	B-OCTYLGLUCOSIDE
2	PO4	4	Ligand/Ion	PHOSPHATE ION
3	SIN	2	Ligand/Ion	SUCCINIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:102 , LYS A:103 , LEU A:110 , THR A:132 , THR A:133 , ARG A:136 , ILE A:140 , CYS A:196 , TYR A:197 , SER A:200 , HOH A:604 , HOH A:678 , HOH A:727	BINDING SITE FOR RESIDUE BOG A 510
2	AC2	SOFTWARE	PHE A:299 , VAL A:375	BINDING SITE FOR RESIDUE BOG A 525
3	AC3	SOFTWARE	ARG A:255 , HIS A:256 , ASN A:262 , ARG A:305 , GLU A:325 , HIS A:390 , GLN A:391 , HOH A:689	BINDING SITE FOR RESIDUE PO4 A 515
4	AC4	SOFTWARE	TYR A:336 , ARG A:350 , LYS A:354 , TYR A:365 , GLN A:391 , ARG A:395 , HOH A:635 , HOH A:642 , HOH A:688 , HOH A:787	BINDING SITE FOR RESIDUE PO4 A 520
5	AC5	SOFTWARE	GLY A:75 , ARG A:78 , PHE A:91 , THR A:130 , ARG A:136 , ARG A:193 , TYR A:197 , HOH A:619 , HOH A:695 , HOH A:714 , HOH A:772	BINDING SITE FOR RESIDUE SIN A 505
6	S1	AUTHOR	GLY A:45 , LEU A:46 , PRO A:47 , ALA A:48 , ARG A:49 , GLY A:50 , LYS A:51 , THR A:52	WALKER-A MOTIF (GXXGXGKT), PART OF THE CLASSICAL MONONUCLEOTIDE BINDING MOTIF.
7	S2	AUTHOR	VAL A:124 , ALA A:125 , VAL A:126 , PHE A:127 , ASP A:128	WALKER-B MOTIF (ZZZZD, Z=HYDROPHOBIC), PART OF THE CLASSICAL MONONUCLEOTIDE BINDING MOTIF. ASP 128 SERVES AS A LIGAND TO THE MG OF MG-ATP.
8	S3	AUTHOR	HIS A:256 , GLU A:325 , HIS A:390	CATALYTIC TRIAD FOR THE FRUCTOSE-2,6- BISPHOSPHATASE REACTION.

(no "SS Bond" information available for 3BIF)

(no "Cis Peptide Bond" information available for 3BIF)

(no "SAP(SNP)/Variant" information available for 3BIF)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	F264_RAT	254-263	1	A:253-262

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	F264_RAT	254-263	2	A:253-262

Asymmetric Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000028039	1	ENSRNOE00000280705	chr8:114012543-114012569	27	F264_RAT	-	0	0	-	-
1.2a	ENSRNOT00000028039	2a	ENSRNOE00000201362	chr8:114012889-114012992	104	F264_RAT	1-33	33	0	-	-
1.3	ENSRNOT00000028039	3	ENSRNOE00000201367	chr8:114019691-114019807	117	F264_RAT	33-72	40	1	A:37-71	35
1.4	ENSRNOT00000028039	4	ENSRNOE00000201368	chr8:114019949-114020045	97	F264_RAT	72-104	33	1	A:71-103	33
1.5	ENSRNOT00000028039	5	ENSRNOE00000201372	chr8:114026200-114026266	67	F264_RAT	104-126	23	1	A:103-125	23
1.6	ENSRNOT00000028039	6	ENSRNOE00000201377	chr8:114028370-114028444	75	F264_RAT	127-151	25	1	A:126-150	25
1.7	ENSRNOT00000028039	7	ENSRNOE00000201385	chr8:114028761-114028817	57	F264_RAT	152-170	19	1	A:151-169	19
1.8	ENSRNOT00000028039	8	ENSRNOE00000201392	chr8:114029422-114029543	122	F264_RAT	171-211	41	1	A:170-210	41
1.10	ENSRNOT00000028039	10	ENSRNOE00000201396	chr8:114031424-114031631	208	F264_RAT	211-280	70	1	A:210-279	70
1.11	ENSRNOT00000028039	11	ENSRNOE00000201403	chr8:114032132-114032278	147	F264_RAT	281-329	49	1	A:280-328	49
1.15	ENSRNOT00000028039	15	ENSRNOE00000201411	chr8:114045247-114045351	105	F264_RAT	330-364	35	1	A:329-363	35
1.16	ENSRNOT00000028039	16	ENSRNOE00000201415	chr8:114047233-114047362	130	F264_RAT	365-408	44	1	A:364-407	44
1.17	ENSRNOT00000028039	17	ENSRNOE00000300921	chr8:114047457-114047519	63	F264_RAT	408-429	22	1	A:407-428	22
1.18	ENSRNOT00000028039	18	ENSRNOE00000348609	chr8:114048504-114048568	65	F264_RAT	429-450	22	1	A:428-449	22
1.19c	ENSRNOT00000028039	19c	ENSRNOE00000365772	chr8:114050180-114050534	355	F264_RAT	451-469	19	1	A:450-468	19

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:432
 aligned with F264_RAT | P25114 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:432
                                    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       347       357       367       377       387       397       407       417       427       437       447       457       467  
             F264_RAT    38 CPTLIVMVGLPARGKTYISKKLTRYLNWIGVPTREFNVGQYRRDMVKTYKSFEFFLPDNEEGLKIRKQCALAALNDVRKFLSEEGGHVAVFDATNTTRERRAMIFNFGEQNGYKTFFVESICVDPEVIAANIVQVKLGSPDYVNRDSDEATEDFMRRIECYENSYESLDEEQDRDLSYIKIMDVGQSYVVNRVADHIQSRIVYYLMNIHVTPRSIYLCRHGESELNLKGRIGGDPGLSPRGREFSKHLAQFISDQNIKDLKVWTSQMKRTIQTAEALSVPYEQWKVLNEIDAGVCEEMTYEEIQDHYPLEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKAAEELPYLKCPLHTVLKLTPVAYGCKVESIFLNVAAVNTHRDRPQNVDISRPSEEALVTVPAHQ 469
               SCOP domains d3bifa1 A:37-249 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain                                                                                                                                 d3bifa2 A:250-468 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, phosphatase domain                                                                                                                                  SCOP domains
               CATH domains 3bifA01 A:37-242 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         ----3bifA02 A:247-467 Phosphoglycerate mutase-like                                                                                                                                                                               - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..............eeeee....eeeee...hhhhhhhhhhhh........eeeee...hhhhhh.........hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh....hhhhh.....eeeeeee....eeeeeee....................hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PG_MUTASE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:37-71 [INCOMPLETE]-------------------------------Exon 1.5  PDB: A:103-12Exon 1.6  PDB: A:126-150 Exon 1.7           ----------------------------------------Exon 1.10  PDB: A:210-279 UniProt: 211-280                            Exon 1.11  PDB: A:280-328 UniProt: 281-329       Exon 1.15  PDB: A:329-363          Exon 1.16  PDB: A:364-407 UniProt: 365-408  --------------------Exon 1.18             Exon 1.19c          Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.4  PDB: A:71-103          ------------------------------------------------------------------Exon 1.8  PDB: A:170-210 UniProt: 171-211----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17             ---------------------------------------- Transcript 1 (2)
                 3bif A  37 CPTLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNVGQYRRDMVKTYKSFEFFLPDNEEGLKIRKQCALAALNDVRKFLSEEGGHVAVFDATNTTRERRAMIFNFGEQNGYKTFFVESICVDPEVIAANIVQVKLGSPDYVNRDSDEATEDFMRRIECYENSYESLDEEQDRDLSYIKIMDVGQSYVVNRVADHIQSRIVYYLMNIHVTPRSIYLCRHGESELNLKGRIGGDPGLSPRGREFSKHLAQFISDQNIKDLKVFTSQMKRTIQTAEALSVPYEQFKVLNEIDAGVCEEMTYEEIQDHYPLEFALRDQDKYRYRYPKGESYEDLVQRLEPVIMELERQENVLVICHQAVMRCLLAYFLDKAAEELPYLKCPLHTVLKLTPVAYGCKVESIFLNVAAVNTHRDRPQNVDISRPSEEALVTVPAHQ 468
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Norway rat (Rattus norvegicus) (38)

3bifA01

A:37-242

Homologous Superfamily: Phosphoglycerate mutase-like (91)

Norway rat (Rattus norvegicus) (10)

3bifA02

A:247-467

(no "Pfam Domain" information available for 3BIF)

Asymmetric Unit(hide GO term definitions)

Chain A (F264_RAT | P25114)

molecular function
	GO:0003873	6-phosphofructo-2-kinase activity	Catalysis of the reaction: beta-D-fructose 6-phosphate + ATP = beta-D-fructose 2,6-bisphosphate + ADP + 2 H(+).
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0004331	fructose-2,6-bisphosphate 2-phosphatase activity	Catalysis of the reaction: D-fructose 2,6-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:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006003	fructose 2,6-bisphosphate metabolic process	The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase.
	GO:0006000	fructose metabolic process	The chemical reactions and pathways involving fructose, the ketohexose arabino-2-hexulose. Fructose exists in a open chain form or as a ring compound. D-fructose is the sweetest of the sugars and is found free in a large number of fruits and honey.
	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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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