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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF A PYROPHOSPHATE-DEPENDENT PHOSPHOFRUCTOKINASE FROM THE LYME DISEASE SPIROCHETE BORRELIA BURGDORFERI

Authors :   S. A. Moore, R. S. Ronimus, R. S. Roberson, H. W. Morgan

Date :   06 Feb 02 (Deposition) - 15 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Phosphofructokinase, Pyrophosphate, Phosphotransferase, Spirochete, Borrelia Burgdorferi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Moore, R. S. Ronimus, R. S. Roberson, H. W. Morgan
The Structure Of A Pyrophosphate-Dependent Phosphofructokinase From The Lyme Disease Spirochete Borrelia Burgdorferi.
Structure V. 10 659 2002
PubMed-ID: 12015149 | Reference-DOI: 10.1016/S0969-2126(02)00760-8
(for further references see the PDB file header)

Molecule 1 - PHOSPHOFRUCTOKINASE
	Chains	:	A, B
	EC Number	:	2.7.1.90
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEX HTB
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BB0020
	Organism Common	:	LYME DISEASE SPIROCHETE
	Organism Scientific	:	BORRELIA BURGDORFERI
	Organism Taxid	:	139
	Synonym	:	PYROPHOSPHATE--FRUCTOSE 6-PHOSPHATE 1- PHOSPHOTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:82 , ARG A:146 , ARG A:431 , THR B:241 , LYS B:243 , TYR B:244	BINDING SITE FOR RESIDUE SO4 A 600
2	AC2	SOFTWARE	ARG A:146 , GLY A:175 , ASP A:176 , ASP A:177 , SER A:178 , LYS A:203 , HOH A:794 , HOH A:801	BINDING SITE FOR RESIDUE SO4 A 601
3	AC3	SOFTWARE	LYS A:71 , ALA A:72 , ASN A:102 , ASN A:104	BINDING SITE FOR RESIDUE SO4 A 602
4	AC4	SOFTWARE	THR A:241 , LYS A:243 , TYR A:244 , ARG B:146 , ARG B:431	BINDING SITE FOR RESIDUE SO4 B 1600
5	AC5	SOFTWARE	SER B:80 , GLY B:81 , ARG B:146 , GLY B:175 , ASP B:177 , SER B:178 , LYS B:203	BINDING SITE FOR RESIDUE SO4 B 1601
6	AC6	SOFTWARE	LYS B:71 , ALA B:72 , ASN B:102 , ASN B:104	BINDING SITE FOR RESIDUE SO4 B 1602
7	AC7	SOFTWARE	HIS A:424 , PHE A:425 , HOH A:759 , HOH A:783 , HIS B:424 , PHE B:425	BINDING SITE FOR RESIDUE SO4 B 1603
8	AC8	SOFTWARE	LYS B:23 , ASP B:24 , ASN B:27 , GLU B:62	BINDING SITE FOR RESIDUE SO4 B 1604

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

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

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

(no "PROSITE Motif" information available for 1KZH)

(no "Exon" information available for 1KZH)

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:550
 aligned with PFP_BORBU | P70826 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:550
                                    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       453       463       473       483       493       503       513       523       533       543       553
            PFP_BORBU     4 SLFKQERQKYIPKLPNILKKDFNNISLVYGENTEAIQDRQALKEFFKNTYGLPIISFTEGESSLSFSKALNIGIILSGGPAPGGHNVISGVFDAIKKFNPNSKLFGFKGGPLGLLENDKIELTESLINSYRNTGGFDIVSSGRTKIETEEHYNKALFVAKENNLNAIIIIGGDDSNTNAAILAEYFKKNGENIQVIGVPKTIDADLRNDHIEISFGFDSATKIYSELIGNLCRDAMSTKKYWHFVKLMGRSASHVALECALKTHPNICIVSEEVLAKKKTLSEIIDEMVSVILKRSLNGDNFGVVIVPEGLIEFIPEVKSLMLELCDIFDKNEGEFKGLNIEKMKEIFVAKLSDYMKGVYLSLPLFIQFELIKSILERDPHGNFNVSRVPTEKLFIEMIQSRLNDMKKRGEYKGSFTPVDHFFGYEGRSAFPSNFDSDYCYSLGYNAVVLILNGLTGYMSCIKNLNLKPTDWIAGGVPLTMLMNMEERYGEKKPVIKKALVDLEGRPFKEFVKNRDKWALNNLYLYPGPVQYFGSSEIVDEITETLKLEL 553
               SCOP domains d1kzha_ A: Pyrophosphate-dependent phosphofructokinase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1kzhA01 A:5-219,A:432-501  [code=3.40.50.450, no name defined]                                                                                                                                                         1kzhA02 A:220-317,A:393-431,A:502-552  [code=3.40.50.460, no name defined]                        1kzhA03 A:318-392 Phosphofructokinase; domain 3                            1kzhA02 A:220-317,A:393-431,A:502-552  1kzhA01 A:5-219,A:432-501  [code=3.40.50.450, no name defined]        1kzhA02 A:220-317,A:393-431,A:502-552              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh......hhhhhhhhh.eeeeeeee.....hhhhhhhhh......eeeeeee...........eeeeee......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh.eeeehhhhhhhhh................hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh....eeeeeeee.............eehhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh..ee.hhhhhhhh..hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.......eeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhheeeeee....eeeeee..eeeeee........hhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kzh A   4 SLFKQERQKYIPKLPNILKKDFNNISLVYGENTEAIQDRQALKEFFKNTYGLPIISFTEGESSLSFSKALNIGIILSGGPAPGGHNVISGVFDAIKKFNPNSKLFGFKGGPLGLLENDKIELTESLINSYRNTGGFDIVSSGRTKIETEEHYNKALFVAKENNLNAIIIIGGDDSNTNAAILAEYFKKNGENIQVIGVPKTIDADLRNDHIEISFGFDSATKIYSELIGNLCRDAMSTKKYWHFVKLMGRSASHVALECALKTHPNICIVSEEVLAKKKTLSEIIDEMVSVILKRSLNGDNFGVVIVPEGLIEFIPEVKSLMLELCDIFDKNEGEFKGLNIEKMKEIFVAKLSDYMKGVYLSLPLFIQFELIKSILERDPHGNFNVSRVPTEKLFIEMIQSRLNDMKKRGEYKGSFTPVDHFFGYEGRSAFPSNFDSDYCYSLGYNAVVLILNGLTGYMSCIKNLNLKPTDWIAGGVPLTMLMNMEERYGEKKPVIKKALVDLEGRPFKEFVKNRDKWALNNLYLYPGPVQYFGSSEIVDEITETLKLEL 553
                                    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       453       463       473       483       493       503       513       523       533       543       553

Chain B from PDB  Type:PROTEIN  Length:530
 aligned with PFP_BORBU | P70826 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:551
                                    12        22        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       452       462       472       482       492       502       512       522       532       542       552 
            PFP_BORBU     3 TSLFKQERQKYIPKLPNILKKDFNNISLVYGENTEAIQDRQALKEFFKNTYGLPIISFTEGESSLSFSKALNIGIILSGGPAPGGHNVISGVFDAIKKFNPNSKLFGFKGGPLGLLENDKIELTESLINSYRNTGGFDIVSSGRTKIETEEHYNKALFVAKENNLNAIIIIGGDDSNTNAAILAEYFKKNGENIQVIGVPKTIDADLRNDHIEISFGFDSATKIYSELIGNLCRDAMSTKKYWHFVKLMGRSASHVALECALKTHPNICIVSEEVLAKKKTLSEIIDEMVSVILKRSLNGDNFGVVIVPEGLIEFIPEVKSLMLELCDIFDKNEGEFKGLNIEKMKEIFVAKLSDYMKGVYLSLPLFIQFELIKSILERDPHGNFNVSRVPTEKLFIEMIQSRLNDMKKRGEYKGSFTPVDHFFGYEGRSAFPSNFDSDYCYSLGYNAVVLILNGLTGYMSCIKNLNLKPTDWIAGGVPLTMLMNMEERYGEKKPVIKKALVDLEGRPFKEFVKNRDKWALNNLYLYPGPVQYFGSSEIVDEITETLKLEL 553
               SCOP domains d1kzhb_ B: Pyrophosphate-dependent phosphofructokinase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --1kzhB01 B:5-219,B:432-501  [code=3.40.50.450, no name defined]                                                                                                                                                         1kzhB02 B:220-317,B:393-431,B:502-552  [code=3.40.50.460, no name defined]                        1kzhB03 B:318-3           92 Phosphofructokinase; domain 3                 1kzhB02 B:220-317,B:393-431,B:502-552  1kzhB01 B:5-219,B:432-501  [code=3.40.50.450, no name defined]        1kzhB02 B:220-317,B:393-431,B:502-552              - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.....hhhhhhhhh.eeeeeeee.....hhhhhhhhh......eeeeeee...........eeeeee......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhh..eee.hhhhhhhhh................hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh..ee.hhhhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...-----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------..hhhhhhhhhhhhhhhhhhhh.......eeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhheeeeee....eeeeee..eeeeee........hhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kzh B   3 TSLFKQERQKYIPKLPNILKKDFNNISLVYGENTEAIQDRQALKEFFKNTYGLPIISFTEGESSLSFSKALNIGIILSGGPAPGGHNVISGVFDAIKKFNPNSKLFGFKGGPLGLLENDKIELTESLINSYRNTGGFDIVSSGRTKIETEEHYNKALFVAKENNLNAIIIIGGDDSNTNAAILAEYFKKNGENIQVIGVPKTIDADLRNDHIEISFGFDSATKIYSELIGNLCRDAMSTKKYWHFVKLMGRSASHVALECALKTHPNICIVSEEVLAKKKTLSEIIDEMVSVILKRSLNGDNFGVVIVPEGLIEFIPEVKSLMLELCDIF-----------IEKMKEIFVAKLSDYMKGVYLSLPLFIQFELIKSILE----------RVPTEKLFIEMIQSRLNDMKKRGEYKGSFTPVDHFFGYEGRSAFPSNFDSDYCYSLGYNAVVLILNGLTGYMSCIKNLNLKPTDWIAGGVPLTMLMNMEERYGEKKPVIKKALVDLEGRPFKEFVKNRDKWALNNLYLYPGPVQYFGSSEIVDEITETLKLEL 553
                                    12        22        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         - |     352       362       372       | -       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552 
                                                                                                                                                                                                                                                                                                                                                                   332         344                                 380        391

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: Phosphofructokinase (14)

Superfamily: Phosphofructokinase (14)

Family: Phosphofructokinase (13)

Protein domain: Pyrophosphate-dependent phosphofructokinase (1)

Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] (1)

1a	d1kzha_	A:
1b	d1kzhb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.450, no name defined] (19)

Lyme disease spirochete (Borrelia burgdorferi) (1)

1a	1kzhA01	A:5-219,A:432-501
1b	1kzhB01	B:5-219,B:432-501

Homologous Superfamily: [code=3.40.50.460, no name defined] (9)

Lyme disease spirochete (Borrelia burgdorferi) (1)

2a	1kzhA02	A:220-317,A:393-431,A:502-552
2b	1kzhB02	B:220-317,B:393-431,B:502-552

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Phosphofructokinase; domain 3 (2)

Lyme disease spirochete (Borrelia burgdorferi) (1)

3a	1kzhA03	A:318-392
3b	1kzhB03	B:318-392

(no "Pfam Domain" information available for 1KZH)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PFP_BORBU | P70826)

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:0047334	diphosphate-fructose-6-phosphate 1-phosphotransferase activity	Catalysis of the reaction: fructose-6-phosphate + diphosphate = phosphate + fructose-1,6-bisphosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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: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: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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1pfk	1PFK CONTAINS THE SAME PROTEIN COMPLEX WITH ADENOSINE-5'- DIPHOSPHATE, FRUCTOSE-1,6-DIPHOSPHATE AND MAGNESIUM ION

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Ligands, Modified Residues, Ions (1, 8)

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