1KC7 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PHOSPHONOPYRUVATE

Authors :   C. C. Chen, A. Howard, O. Herzberg

Date :   07 Nov 01 (Deposition) - 30 Jan 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Transferase, Phosphotransferase, Kinase, Phosphonopyruvate Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Herzberg, C. C. Chen, S. Liu, A. Tempczyk, A. Howard, M. Wei, D. Ye, D. Dunaway-Mariano
Pyruvate Site Of Pyruvate Phosphate Dikinase: Crystal Structure Of The Enzyme-Phosphonopyruvate Complex, And Mutant Analysis
Biochemistry V. 41 780 2002
PubMed-ID: 11790099 | Reference-DOI: 10.1021/BI011799+
(for further references see the PDB file header)

Molecule 1 - PYRUVATE PHOSPHATE DIKINASE
	Chains	:	A
	EC Number	:	2.7.9.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PACYC184-D12
	Expression System Strain	:	JM 101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PPDK
	Organism Scientific	:	CLOSTRIDIUM SYMBIOSUM
	Organism Taxid	:	1512
	Synonym	:	PPDK

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	PPR	1	Ligand/Ion	PHOSPHONOPYRUVATE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PPR	2	Ligand/Ion	PHOSPHONOPYRUVATE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PPR	2	Ligand/Ion	PHOSPHONOPYRUVATE
3	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:745 , ASP A:769 , PPR A:1000	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	LYS A:22 , MET A:99 , PRO A:100 , GLY A:101 , MET A:102 , MET A:103 , ARG A:337	BINDING SITE FOR RESIDUE SO4 A 1002
3	AC3	SOFTWARE	ARG A:523 , TRP A:527	BINDING SITE FOR RESIDUE SO4 A 1003
4	AC4	SOFTWARE	LYS A:718 , GLU A:758 , ARG A:823	BINDING SITE FOR RESIDUE SO4 A 1004
5	AC5	SOFTWARE	PRO A:660 , MET A:661 , ARG A:665	BINDING SITE FOR RESIDUE SO4 A 1005
6	AC6	SOFTWARE	ARG A:561 , ARG A:617 , MET A:743 , GLU A:745 , GLY A:766 , THR A:767 , ASN A:768 , ASP A:769 , GLY A:832 , MG A:1001	BINDING SITE FOR RESIDUE PPR A 1000

(no "SS Bond" information available for 1KC7)

(no "Cis Peptide Bond" information available for 1KC7)

(no "SAP(SNP)/Variant" information available for 1KC7)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEP_ENZYMES_PHOS_SITE	PS00370	PEP-utilizing enzymes phosphorylation site signature.	PPDK_CLOSY	450-461	1	A:450-461
2	PEP_ENZYMES_2	PS00742	PEP-utilizing enzymes signature 2.	PPDK_CLOSY	761-779	1	A:761-779

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEP_ENZYMES_PHOS_SITE	PS00370	PEP-utilizing enzymes phosphorylation site signature.	PPDK_CLOSY	450-461	2	A:450-461
2	PEP_ENZYMES_2	PS00742	PEP-utilizing enzymes signature 2.	PPDK_CLOSY	761-779	2	A:761-779

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEP_ENZYMES_PHOS_SITE	PS00370	PEP-utilizing enzymes phosphorylation site signature.	PPDK_CLOSY	450-461	2	A:450-461
2	PEP_ENZYMES_2	PS00742	PEP-utilizing enzymes signature 2.	PPDK_CLOSY	761-779	2	A:761-779

(no "Exon" information available for 1KC7)

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:872
 aligned with PPDK_CLOSY | P22983 from UniProtKB/Swiss-Prot  Length:874

    Alignment length:872
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871  
           PPDK_CLOSY     2 AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNN 873
               SCOP domains d1kc7a3 A:2-376 Pyruvate phosphate dikinase, N-terminal domain                                                                                                                                                                                                                                                                                                                         d1kc7a2 A:377-509 Pyruvate phosphate dikinase, central domain                                                                        d1kc7a1 A:510-873 Pyruvate phosphate dikinase, C-terminal domain                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1kc7A01 A:2-109,A:199-243 ATP-grasp fold, A domain                                                          1kc7A05 A:110-198  [code=1.20.80.30, no name defined]                                    1kc7A01 A:2-109,A:199-243                    1kc7A06 A:244-341 ATP-grasp fold, B domain                                                        1kc7A02 A:342-382,A:510-531              1kc7A03 A:383-507 Phosphohistidine domains of PEP-utilising enzymes                                                          --1kc7A02               1kc7A04 A:532-873 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------PPDK_N-1kc7A03 A:10-362                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------PEP-utilizers-1kc7A02 A:412-503                                                             -----------PEP-utilizers_C-1kc7A01 A:515-871                                                                                                                                                                                                                                                                                                                                    -- Pfam domains
         Sec.struct. author ...eee.hhh...hhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.ee.....ee.eeeeee..........eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhh.eeeeee..........eeeeeeee......eeeeeeeee..hhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.eehhhhhhh..eeee.eeee..eeeeeee.hhhhhhhhhhh...eeeee...hhhhhhhhhhh.eeee......hhhhhhhhhhh.eeee.....eee....eeee..eeee...eeeee....eeee....ee......hhhhhhhhhhhhh..eeee...hhhhhhhhhhh....eeee..hhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhh....eeeehhhhhhhhhhh.hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEP_ENZYMES_2      ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kc7 A   2 AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNN 873
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871

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(hide GO term definitions)

Chain A (PPDK_CLOSY | P22983)

molecular function
	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: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: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:0050242	pyruvate, phosphate dikinase activity	Catalysis of the reaction: ATP + phosphate + pyruvate = AMP + diphosphate + 2 H(+) + phosphoenolpyruvate.
	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.
	GO:0016772	transferase activity, transferring phosphorus-containing groups	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
	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.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1kc7)

Biological Units
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	1kc7
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	PPDK_CLOSY \| P22983
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	2.7.9.1
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UniProtKB/Swiss-Prot
	PPDK_CLOSY \| P22983	:	1dik 1ggo 1jde 1kbl 2dik 2fm4 2r82

1dik	1DIK IS PYRUVATE PHOSPHATE DIKINASE (ROOM TEMPERATURE DATA).
1kbl	1KBL IS PYRUVATE PHOSPHATE DIKINASE (100K SYNCHROTRON DATA).

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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