3UQE - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PHOSPHOFRUCTOKINASE-2 MUTANT Y23D FROM ESCHERICHIA COLI

Authors :   H. M. Pereira, A. Caniuguir, M. Baez, R. Cabrera, R. C. Garatt, J. Babul

Date :   20 Nov 11 (Deposition) - 21 Nov 12 (Release) - 21 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Phosphofructokinases, Pfk-2, Glycolysis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. M. Pereira, A. Caniuguir, M. Baez, R. Cabrera, R. C. Garratt, J. Babu
Structure Of E. Coli Pfk2 Mutant Y23D
To Be Published
PubMed: search

Molecule 1 - 6-PHOSPHOFRUCTOKINASE ISOZYME 2
	Chains	:	A, B
	EC Number	:	2.7.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21-D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1723, JW5280, PFK2, PFKB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PHOSPHOFRUCTOKINASE-2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	POP	4	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:185 , ASN A:187 , SER A:224 , LEU A:225 , GLY A:226 , PRO A:227 , GLY A:229 , SER A:248 , ALA A:254 , GLY A:255 , MET A:258 , VAL A:280 , GLY A:283 , SER A:284 , THR A:287 , MG A:402 , MG A:403 , POP A:404 , HOH A:505 , HOH A:510 , HOH A:519 , HOH A:536 , HOH A:569 , HOH A:574 , HOH A:577 , HOH A:604 , LYS B:27	BINDING SITE FOR RESIDUE ATP A 401
2	AC2	SOFTWARE	ATP A:401 , POP A:404 , HOH A:574	BINDING SITE FOR RESIDUE MG A 402
3	AC3	SOFTWARE	ASP A:166 , GLU A:190 , ATP A:401 , HOH A:533 , HOH A:568 , HOH A:569 , HOH A:570 , HOH A:598	BINDING SITE FOR RESIDUE MG A 403
4	AC4	SOFTWARE	ASN A:187 , LYS A:189 , ATP A:401 , MG A:402 , HOH A:569 , LYS B:27 , HOH B:599	BINDING SITE FOR RESIDUE POP A 404
5	AC5	SOFTWARE	ASP B:166 , ATP B:404 , HOH B:553 , HOH B:554 , HOH B:556 , HOH B:582	BINDING SITE FOR RESIDUE MG B 401
6	AC6	SOFTWARE	GLY A:26 , LYS A:27 , ASN B:187 , MG B:403 , ATP B:404 , HOH B:507 , HOH B:554	BINDING SITE FOR RESIDUE POP B 402
7	AC7	SOFTWARE	ASN B:187 , POP B:402 , ATP B:404 , HOH B:591	BINDING SITE FOR RESIDUE MG B 403
8	AC8	SOFTWARE	LYS A:27 , LYS B:185 , ASN B:187 , SER B:224 , LEU B:225 , GLY B:226 , PRO B:227 , GLY B:229 , SER B:248 , ALA B:254 , GLY B:255 , MET B:258 , VAL B:280 , GLY B:283 , SER B:284 , THR B:287 , MG B:401 , POP B:402 , MG B:403 , HOH B:503 , HOH B:507 , HOH B:508 , HOH B:520 , HOH B:543 , HOH B:554 , HOH B:556 , HOH B:591 , HOH B:609	BINDING SITE FOR RESIDUE ATP B 404

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

Asymmetric Unit

No.	Residues
1	Val A:252	-	Gly A:253

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	PFKB_ECOLI	38-62	2	A:38-62 B:38-62
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	PFKB_ECOLI	250-263	2	A:250-263 B:250-263

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	PFKB_ECOLI	38-62	4	A:38-62 B:38-62
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	PFKB_ECOLI	250-263	4	A:250-263 B:250-263

(no "Exon" information available for 3UQE)

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:307
 aligned with PFKB_ECOLI | P06999 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         
           PFKB_ECOLI     1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR 309
               SCOP domains d3uqea_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeeeee..............eeeeehhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh....eeeee........eeeee....eeeee.......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......ee..hhhhhhhhhh......hhhhhhhhhhhhh.....eeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...--...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uqe A   1 MVRIYTLTLAPSLDSATITPQIDPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQ--RLCSHDDTQKIYAYLSR 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         
                                                                                                                                                                                                                                                                                                                           290  |                
                                                                                                                                                                                                                                                                                                                              293

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with PFKB_ECOLI | P06999 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         
           PFKB_ECOLI     1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQKIYAYLSR 309
               SCOP domains d3uqeb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeeeee..............eeeeehhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh...eeeee........eeeee.....eeee.......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.....ee..hhhhhhhhhh......hhhhhhhhhhhhh.....eeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.----...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uqe B   1 MVRIYTLTLAPSLDSATITPQIDPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEEQVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATL----RLCSHDDTQKIYAYLSR 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       | -  |    300         
                                                                                                                                                                                                                                                                                                                         288  293

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Escherichia coli K-12 [TaxId: 83333] (5)

1a	d3uqea_	A:
1b	d3uqeb_	B:

(no "CATH Domain" information available for 3UQE)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PFKB_ECOLI | P06999)

molecular function
	GO:0003872	6-phosphofructokinase activity	Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0009024	tagatose-6-phosphate kinase activity	Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
	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: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:0006974	cellular response to DNA damage stimulus	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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	GO:0061615	glycolytic process through fructose-6-phosphate	The chemical reactions and pathways resulting in the breakdown of a monosaccharide into pyruvate, occurring through a fructose-6-phosphate intermediate, with the concomitant production of ATP and NADH.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Val A:252 - Gly A:253	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	3uqe
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	2.7.1.11
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	PFKB_ECOLI \| P06999	:	3cqd 3n1c 3umo 3ump 3uqd

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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