2DWP - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   A PSEUDO SUBSTRATE COMPLEX OF 6-PHOSPHOFRUCTO-2-KINASE OF PFKFB

Authors :   Y. H. Lee

Date :   16 Aug 06 (Deposition) - 03 Jul 07 (Release) - 06 May 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   A Ternary Complex, Amppcp, Fructose-6-Phosphate, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. G. Kim, M. Cavalier, M. R. El-Maghrabi, Y. H. Lee
A Direct Substrate-Substrate Interaction Found In The Kinase Domain Of The Bifunctional Enzyme, 6-Phosphofructo-2-Kinase/Fructose-2, 6- Bisphosphatase
J. Mol. Biol. V. 370 14 2007
PubMed-ID: 17499765 | Reference-DOI: 10.1016/J.JMB.2007.03.038
(for further references see the PDB file header)

Molecule 1 - 6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6- BIPHOSPHATASE 3
	Chains	:	A
	EC Number	:	2.7.1.105, 3.1.3.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PFKFB3, PHOSPHORYL TRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	F6P	2	Ligand/Ion	FRUCTOSE-6-PHOSPHATE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ACP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	F6P	4	Ligand/Ion	FRUCTOSE-6-PHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACP	1	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	F6P	2	Ligand/Ion	FRUCTOSE-6-PHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:43 , GLY A:71 , ARG A:74 , ARG A:98 , ALA A:125 , THR A:126 , ARG A:132 , ARG A:189 , TYR A:193 , ACP A:700 , HOH A:755 , HOH A:769 , HOH A:775	BINDING SITE FOR RESIDUE F6P A 702
2	AC2	SOFTWARE	ARG A:252 , ILE A:264 , GLY A:265 , GLU A:322 , TYR A:333 , ARG A:347 , LYS A:351 , TYR A:362 , GLN A:388 , ARG A:392 , THR A:440 , HOH A:758 , HOH A:763 , HOH A:823 , HOH A:839 , HOH A:861 , HOH A:885	BINDING SITE FOR RESIDUE F6P A 720
3	AC3	SOFTWARE	THR A:48 , ACP A:700 , HOH A:743 , HOH A:913	BINDING SITE FOR RESIDUE MG A 701
4	AC4	SOFTWARE	PRO A:43 , ALA A:44 , ARG A:45 , GLY A:46 , LYS A:47 , THR A:48 , TYR A:49 , SER A:152 , ASN A:163 , GLU A:166 , VAL A:167 , LYS A:168 , PHE A:186 , VAL A:243 , TYR A:424 , MG A:701 , F6P A:702 , HOH A:1004	BINDING SITE FOR RESIDUE ACP A 700

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	F263_HUMAN	251-260	1	A:250-259

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.	F263_HUMAN	251-260	2	A:250-259

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PG_MUTASE	PS00175	Phosphoglycerate mutase family phosphohistidine signature.	F263_HUMAN	251-260	1	A:250-259

Asymmetric Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3d	ENST00000379775	3d	ENSE00001911115	chr10:6244894-6245299	406	F263_HUMAN	1-26	26	1	A:3-19	17
1.4	ENST00000379775	4	ENSE00001636131	chr10:6255586-6255711	126	F263_HUMAN	26-68	43	1	A:32-67	36
1.5	ENST00000379775	5	ENSE00001691710	chr10:6257184-6257280	97	F263_HUMAN	68-100	33	1	A:67-99	33
1.6	ENST00000379775	6	ENSE00001625550	chr10:6258088-6258154	67	F263_HUMAN	100-122	23	1	A:99-121	23
1.7	ENST00000379775	7	ENSE00001748558	chr10:6258669-6258743	75	F263_HUMAN	123-147	25	1	A:122-146	25
1.8	ENST00000379775	8	ENSE00001650689	chr10:6259098-6259154	57	F263_HUMAN	148-166	19	1	A:147-165	19
1.9	ENST00000379775	9	ENSE00001672633	chr10:6261532-6261656	125	F263_HUMAN	167-208	42	1	A:166-207	42
1.10	ENST00000379775	10	ENSE00001727947	chr10:6262621-6262828	208	F263_HUMAN	208-277	70	1	A:207-276	70
1.11a	ENST00000379775	11a	ENSE00001665756	chr10:6263344-6263490	147	F263_HUMAN	278-326	49	1	A:277-325	49
1.12	ENST00000379775	12	ENSE00001758318	chr10:6263604-6263708	105	F263_HUMAN	327-361	35	1	A:326-360	35
1.13b	ENST00000379775	13b	ENSE00001626155	chr10:6264818-6264947	130	F263_HUMAN	362-405	44	1	A:361-404	44
1.14	ENST00000379775	14	ENSE00001771643	chr10:6265921-6265983	63	F263_HUMAN	405-426	22	1	A:404-425	22
1.15a	ENST00000379775	15a	ENSE00001800461	chr10:6266112-6266176	65	F263_HUMAN	426-447	22	1	A:425-445	21
1.18a	ENST00000379775	18a	ENSE00001683359	chr10:6268155-6268328	174	F263_HUMAN	448-505	58	0	-	-
1.22g	ENST00000379775	22g	ENSE00001643662	chr10:6274858-6277495	2638	F263_HUMAN	506-520	15	0	-	-

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:431
 aligned with F263_HUMAN | Q16875 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:443
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443   
           F263_HUMAN     4 ELTQSRVQKIWVPVDHRPSLPRSCGPKLTNSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERS 446
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------2dwpA01 A:33-243 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                              2dwpA02 A:244-445 Phosphoglycerate mutase-like                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eee....------------...eeeeee.....hhhhhhhhhhhhhhhh...eeeeehhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhh..............eeeeee....eeeee...hhhhhhhhhhhh........eeeee...hhhhhhh........hhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhh....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhh.....hhhhh.....eeeeeeee..eeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PG_MUTASE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3d  PDB: A:3-19 -----------------------------------------Exon 1.5  PDB: A:67-99           ----------------------Exon 1.7  PDB: A:122-146 Exon 1.8           -----------------------------------------Exon 1.10  PDB: A:207-276 UniProt: 208-277                            Exon 1.11a  PDB: A:277-325 UniProt: 278-326      Exon 1.12  PDB: A:326-360          Exon 1.13b  PDB: A:361-404 UniProt: 362-405 --------------------Exon 1.15a            Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.4  PDB: A:32-67 UniProt: 26-68      -------------------------------Exon 1.6  PDB: A:99-121--------------------------------------------Exon 1.9  PDB: A:166-207 UniProt: 167-208 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14             -------------------- Transcript 1 (2)
                 2dwp A   3 ELTQSRVQKIWVPVDHR------------NSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERS 445
                                    12      |  -        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442   
                                           19           32

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 "SCOP Domain" information available for 2DWP)

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)

Human (Homo sapiens) (413)

2dwpA01

A:33-243

Homologous Superfamily: Phosphoglycerate mutase-like (91)

Human (Homo sapiens) (18)

2dwpA02

A:244-445

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

Asymmetric Unit(hide GO term definitions)

Chain A (F263_HUMAN | Q16875)

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:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0061621	canonical glycolysis	The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric Unit
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	2dwp
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	F263_HUMAN \| Q16875
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	2.7.1.105
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Ligands, Modified Residues, Ions (3, 4)

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