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Title :   CRYSTAL STRUCTURE OF A PHOSPHOFRUCTOKINASE FROM PYROCOCCUS HORIKOSHII OT3 WITH AMP

Authors :   A. U. Singer, T. Skarina, S. Kochinyan, G. Brown, M. E. Cuff, A. M. Edward A. Joachimiak, A. Savchenko, A. F. Yakunin, Z. Jia, Midwest Center F Structural Genomics (Mcsg)

Date :   11 Jul 08 (Deposition) - 23 Dec 08 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   6-Phosphofructokinase, Pyrococcus Horikoshii, Amp, Adp, Glycolysis, Kinase, Magnesium, Metal-Binding, Transferase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Currie, F. Merino, T. Skarina, A. H. Wong, A. Singer, G. Brown, A. Savchenko, A. Caniuguir, V. Guixe, A. F. Yakunin, Z. Jia
Adp-Dependent 6-Phosphofructokinase From Pyrococcus Horikoshii Ot3: Structure Determination And Biochemical Characterization Of Ph1645.
J. Biol. Chem. V. 284 22664 2009
PubMed-ID: 19553681 | Reference-DOI: 10.1074/JBC.M109.012401

Molecule 1 - ADP-SPECIFIC PHOSPHOFRUCTOKINASE
	Chains	:	A, B
	EC Number	:	2.7.1.146
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PHOSPHOFRUCTOKINASE
	Gene	:	PFKC, PH1645
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953
	Strain	:	OT3
	Synonym	:	ADP-DEPENDENT PHOSPHOFRUCTOKINASE, ADP-PFK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:336 , THR A:337 , ARG A:420 , LEU A:421 , VAL A:422 , LEU A:431 , ILE A:435 , NA A:1486 , HOH A:1641 , HOH A:1656 , HOH A:1730	BINDING SITE FOR RESIDUE AMP A 1484
2	AC2	SOFTWARE	THR A:104 , ARG A:369 , ILE A:375	BINDING SITE FOR RESIDUE NA A 1485
3	AC3	SOFTWARE	LEU A:431 , GLY A:432 , AMP A:1484	BINDING SITE FOR RESIDUE NA A 1486
4	AC4	SOFTWARE	HIS B:335 , THR B:336 , THR B:337 , THR B:419 , ARG B:420 , LEU B:421 , VAL B:422 , LEU B:431 , GLY B:432 , ILE B:435 , HOH B:1707 , HOH B:1785	BINDING SITE FOR RESIDUE AMP B 1485

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:11	-	Tyr A:12
2	Ala B:11	-	Tyr B:12

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADPK	PS51255	ADP-dependent kinase (ADPK) domain profile.	K6PF_PYRHO	1-449	2	A:1-449 B:1-449

(no "Exon" information available for 3DRW)

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:460
 aligned with K6PF_PYRHO | O59355 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:460
                                      1                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                     -|       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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
           K6PF_PYRHO     - ----------MIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450
               SCOP domains d3drwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3drwA01                3drwA02 A:14-95,A:156-192  [code=3.30.1110.20, no name defined]                   3drwA01 A:-10-13,A:96-155,A:193-450                         3drwA02 A:14-95,A:156-192            3drwA01 A:-10-13,A:96-155,A:193-450  [code=3.40.1190.20, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee...eeeeeee.hhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeehhhhhhhhhhhhh...eeee.....hhhhhh.....eeeeee....eeeee.hhh........eeeeeee....eee....eee....eeeeeee..hhhhh......hhhhhhhhhhhh.eeee.hhhhh........hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------ADPK  PDB: A:1-449 UniProt: 1-449                                                                                                                                                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3drw A -10 SGRENLYFQGMIPEHLSIYTAYNANIAAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450
                                    -1|       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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
                                    -1|                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                      1

Chain B from PDB  Type:PROTEIN  Length:450
 aligned with K6PF_PYRHO | O59355 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:450
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
           K6PF_PYRHO     1 MIPEHLSIYTAYNANIDAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450
               SCOP domains d3drwb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3drwB01      3drwB02 B:14-95,B:156-192  [code=3.30.1110.20, no name defined]                   3drwB01 B:1-13,B:96-155,B:193-450                           3drwB02 B:14-95,B:156-192            3drwB01 B:1-13,B:96-155,B:193-450  [code=3.40.1190.20, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...eeeeeee.hhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeehhhhhhhhhhhhh...eeeee....hhhhhh.....eeeeeee..eeeeee.hhh........eeeeeee....eeee..eeee....eeeeeee..hhhhh......hhhhhhhhhhhh.eeee.hhhhh........hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeee......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ADPK  PDB: B:1-449 UniProt: 1-449                                                                                                                                                                                                                                                                                                                                                                                                                                - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3drw B   1 MIPEHLSIYTAYNANIAAIVKLNQETIQNLINAFDPDEVKRRIEEYPREINEPIDFVARLVHTLKLGKPAAVPLVNEKMNEWFDKTFRYEEERLGGQAGIIANTLAGLKIRKVIAYTPFLPKRLAELFKKGVLYPVVENGELQFKPIQEAYREGDPLKINRIFEFRKGLKFKLGDETIEIPNSGRFIVSARFESISRIETREDIKPFLGEIGKEVDGAIFSGYQGLRTKYSDGKDANYYLRRAKEDIIEFKEKDVKIHVEFASVQDRKLRKKIITNILPFVDSVGIDEAEIAQILSVLGYRELADRIFTYNRLEDSILGGMIILDELNFEILQVHTTYYLMYITHRDNPLSEEELAKSLEFGTTLAAARASLGDIRGPDDYKVGLKVPFNERSEYVKLRFEEAKSRLRMREYKVVVIPTRLVQNPVLTVGLGDTISAGAFLTYLEFLKRH 450
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450

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/Biological 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: ADP-specific Phosphofructokinase/Glucokinase (5)

Protein domain: automated matches (1)

Pyrococcus horikoshii [TaxId: 53953] (1)

1a	d3drwa_	A:
1b	d3drwb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Adenosine kinase, small domain (17)

Homologous Superfamily: [code=3.30.1110.20, no name defined] (5)

Pyrococcus horikoshii. Organism_taxid: 53953. Strain: ot3. (1)

1a	3drwA02	A:14-95,A:156-192
1b	3drwB02	B:14-95,B:156-192

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

Topology: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (109)

Homologous Superfamily: [code=3.40.1190.20, no name defined] (73)

Pyrococcus horikoshii. Organism_taxid: 53953. Strain: ot3. (1)

2a	3drwB01	B:1-13,B:96-155,B:193-450
2b	3drwA01	A:-10-13,A:96-155,A:193-450

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (K6PF_PYRHO | O59355)

molecular function
	GO:0043844	ADP-specific phosphofructokinase activity	Catalysis of the reaction: ADP + D-fructose 6-phosphate = AMP + D-fructose 1,6-bisphosphate.
	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:0008443	phosphofructokinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a fructose substrate molecule.
	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: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: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: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: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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:11 - Tyr A:12	[ RasMol ]
		Ala B:11 - Tyr B:12	[ RasMol ]

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	K6PF_PYRHO \| O59355	:	1u2x

1u2x	CRYSTAL STRUCTURE OF A HYPOTHETICAL ADP-DEPENDENT PHOSPHOFRUCTOKINASE FROM PYROCOCCUS HORIKOSHII OT3 RELATED ID: APC5054 RELATED DB: TARGETDB

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

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Cis Peptide Bonds (2, 2)

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