1A3X - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PG, MN2+ AND K+

Authors :   M. S. Jurica, A. Mesecar, P. J. Heath, W. Shi, T. Nowak, B. L. Stoddard

Date :   26 Jan 98 (Deposition) - 27 May 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Pyruvate Kinase, Allosteric Regulation, Tranferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Jurica, A. Mesecar, P. J. Heath, W. Shi, T. Nowak, B. L. Stoddard
The Allosteric Regulation Of Pyruvate Kinase By Fructose-1, 6-Bisphosphate.
Structure V. 6 195 1998
PubMed-ID: 9519410 | Reference-DOI: 10.1016/S0969-2126(98)00021-5

Molecule 1 - PYRUVATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.40
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	PGA	2	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PGA	2	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PGA	1	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:49 , LYS A:240 , GLU A:242 , ALA A:263 , ARG A:264 , GLY A:265 , ASP A:266 , THR A:298 , MN A:1001 , K A:1002	BINDING SITE FOR RESIDUE PGA A 1005
2	AC2	SOFTWARE	ARG B:49 , SER B:213 , LYS B:240 , GLU B:242 , ALA B:263 , ARG B:264 , GLY B:265 , ASP B:266 , ALA B:297 , THR B:298 , MN B:1003 , K B:1004	BINDING SITE FOR RESIDUE PGA B 1006
3	AC3	SOFTWARE	GLU A:242 , ASP A:266 , PGA A:1005	BINDING SITE FOR RESIDUE MN A 1001
4	AC4	SOFTWARE	ASN A:51 , SER A:53 , ASP A:84 , THR A:85 , SER A:213 , LYS A:240 , PGA A:1005	BINDING SITE FOR RESIDUE K A 1002
5	AC5	SOFTWARE	GLU B:242 , ASP B:266 , PGA B:1006	BINDING SITE FOR RESIDUE MN B 1003
6	AC6	SOFTWARE	ASN B:51 , SER B:53 , ASP B:84 , THR B:85 , SER B:213 , PGA B:1006	BINDING SITE FOR RESIDUE K B 1004

(no "SS Bond" information available for 1A3X)

(no "Cis Peptide Bond" information available for 1A3X)

(no "SAP(SNP)/Variant" information available for 1A3X)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRUVATE_KINASE	PS00110	Pyruvate kinase active site signature.	KPYK1_YEAST	235-247	2	A:235-247 B:235-247

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRUVATE_KINASE	PS00110	Pyruvate kinase active site signature.	KPYK1_YEAST	235-247	4	A:235-247 B:235-247

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRUVATE_KINASE	PS00110	Pyruvate kinase active site signature.	KPYK1_YEAST	235-247	2	A:235-247 B:235-247

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YAL038W	1	YAL038W.1	I:71787-73289	1503	KPYK1_YEAST	1-500	500	2	A:1-500 (gaps) B:1-500 (gaps)	500 500

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:487
 aligned with KPYK1_YEAST | P00549 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:500
                                    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       460       470       480       490       500
          KPYK1_YEAST     1 MSRLERLTSLNVVAGSDLRRTSIIGTIGPKTNNPETLVALRKAGLNIVRMNFSHGSYEYHKSVIDNARKSEELYPGRPLAIALDTKGPEIRTGTTTNDVDYPIPPNHEMIFTTDDKYAKACDDKIMYVDYKNITKVISAGRIIYVDDGVLSFQVLEVVDDKTLKVKALNAGKICSHKGVNLPGTDVDLPALSEKDKEDLRFGVKNGVHMVFASFIRTANDVLTIREVLGEQGKDVKIIVKIENQQGVNNFDEILKVTDGVMVARGDLGIEIPAPEVLAVQKKLIAKSNLAGKPVICATQMLESMTYNPRPTRAEVSDVGNAILDGADCVMLSGETAKGNYPINAVTTMAETAVIAEQAIAYLPNYDDMRNCTPKPTSTTETVAASAVAAVFEQKAKAIIVLSTSGTTPRLVSKYRPNCPIILVTRCPRAARFSHLYRGVFPFVFEKEPVSDWTDDVEARINFGIEKAKEFGILKKGDTYVSIQGFKAGAGHSNTLQVSTV 500
               SCOP domains d1a3xa2 A:1-87,A:189-366 Pyruvate kinase, N-terminal domain                            d1a3xa1 A:88-188 Pyruvate kinase (PK)                                                                d1a3xa2 A:1-87,A:189-366 Pyruvate kinase, N-terminal domain                                                                                                                       d1a3xa3 A:367-500 Pyruvate kinase, C-terminal domain                                                                                   SCOP domains
               CATH domains 1a3xA01           1a3xA02 A:19-87,A:190-355 Phosphoenolpyruvate-binding domains        1a3xA03 A:88-189 M1 Pyruvate Kinase; Domain 3                                                         1a3xA02 A:19-87,A:190-355 Phosphoenolpyruvate-binding domains                                                                                                         1a3xA01 A:1-18,A:356-500  [code=3.40.1380.20, no name defined]                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...............eeee.......hhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhh..................................eeeee....................hhhh.....eeee....eeeee.......eeeeee...........eeee..........hhhhhhhhhhhh.............hhhhhhhhhhh.hhh.....eeee..hhhh..hhhhhhh..eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..eeeee....hhhh......hhhhhhhhhhhh.........hhhh....hhhhhhhhhhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhhh.............hhhhhhhh.....eeeee..hhhhhhhhh...eeeee....-----...hhhhhhhhhhhhhhh..............--------........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRUVATE_KINA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-500 (gaps) UniProt: 1-500                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Transcript 1
                 1a3x A   1 MSRLERLTSLNVVAGSDLRRTSIIGTIGPKTNNPETLVALRKAGLNIVRMNFSHGSYEYHKSVIDNARKSEELYPGRPLAIALDTKGPEIRTGTTTNDVDYPIPPNHEMIFTTDDKYAKACDDKIMYVDYKNITKVISAGRIIYVDDGVLSFQVLEVVDDKTLKVKALNAGKICSHKGVNLPGTDVDLPALSEKDKEDLRFGVKNGVHMVFASFIRTANDVLTIREVLGEQGKDVKIIVKIENQQGVNNFDEILKVTDGVMVARGDLGIEIPAPEVLAVQKKLIAKSNLAGKPVICATQMLESMTYNPRPTRAEVSDVGNAILDGADCVMLSGETAKGNYPINAVTTMAETAVIAEQAIAYLPNYDDMRNCTPKPTSTTETVAASAVAAVFEQKAKAIIVLSTSGTTPRLVSKYRPNCPIILVTRCPRAARFSHLYRGVFPFVFEKE-----TDDVEARINFGIEKAKEFGILKKGDTYVSIQG--------NTLQVSTV 500
                                    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      |  -  |    460       470       480   |     -  |    500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        447   453                            484      493

Chain B from PDB  Type:PROTEIN  Length:487
 aligned with KPYK1_YEAST | P00549 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:500
                                    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       460       470       480       490       500
          KPYK1_YEAST     1 MSRLERLTSLNVVAGSDLRRTSIIGTIGPKTNNPETLVALRKAGLNIVRMNFSHGSYEYHKSVIDNARKSEELYPGRPLAIALDTKGPEIRTGTTTNDVDYPIPPNHEMIFTTDDKYAKACDDKIMYVDYKNITKVISAGRIIYVDDGVLSFQVLEVVDDKTLKVKALNAGKICSHKGVNLPGTDVDLPALSEKDKEDLRFGVKNGVHMVFASFIRTANDVLTIREVLGEQGKDVKIIVKIENQQGVNNFDEILKVTDGVMVARGDLGIEIPAPEVLAVQKKLIAKSNLAGKPVICATQMLESMTYNPRPTRAEVSDVGNAILDGADCVMLSGETAKGNYPINAVTTMAETAVIAEQAIAYLPNYDDMRNCTPKPTSTTETVAASAVAAVFEQKAKAIIVLSTSGTTPRLVSKYRPNCPIILVTRCPRAARFSHLYRGVFPFVFEKEPVSDWTDDVEARINFGIEKAKEFGILKKGDTYVSIQGFKAGAGHSNTLQVSTV 500
               SCOP domains d1a3xb2 B:1-87,B:189-366 Pyruvate kinase, N-terminal domain                            d1a3xb1 B:88-188 Pyruvate kinase (PK)                                                                d1a3xb2 B:1-87,B:189-366 Pyruvate kinase, N-terminal domain                                                                                                                       d1a3xb3 B:367-500 Pyruvate kinase, C-terminal domain                                                                                   SCOP domains
               CATH domains 1a3xB01           1a3xB02 B:19-87,B:190-355 Phosphoenolpyruvate-binding domains        1a3xB03 B:88-189 M1 Pyruvate Kinase; Domain 3                                                         1a3xB02 B:19-87,B:190-355 Phosphoenolpyruvate-binding domains                                                                                                         1a3xB01 B:1-18,B:356-498  [code=3.40.1380.20, no name defined]                                                                                 -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...............eeee.......hhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhh......eeeee.......................eeeee....................hhhh.....eeee....eeeee.......eeeeee...........eeee..........hhhhhhhhhhhh.............hhhhhhhhhhh.hhh.....eeee..hhhh..hhhhhhh..eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..eeeee....hhhh......hhhhhhhhhhhh.........hhhh....hhhhhhhhhhhhhhhh....hhhhhhhhh........hhhhhhhhhhhhhhhh......eee....hhhhhhh......eeeee..hhhhhhhhh...eeeee....-----...hhhhhhhhhhhhhhh..............--------........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRUVATE_KINA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-500 (gaps) UniProt: 1-500                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Transcript 1
                 1a3x B   1 MSRLERLTSLNVVAGSDLRRTSIIGTIGPKTNNPETLVALRKAGLNIVRMNFSHGSYEYHKSVIDNARKSEELYPGRPLAIALDTKGPEIRTGTTTNDVDYPIPPNHEMIFTTDDKYAKACDDKIMYVDYKNITKVISAGRIIYVDDGVLSFQVLEVVDDKTLKVKALNAGKICSHKGVNLPGTDVDLPALSEKDKEDLRFGVKNGVHMVFASFIRTANDVLTIREVLGEQGKDVKIIVKIENQQGVNNFDEILKVTDGVMVARGDLGIEIPAPEVLAVQKKLIAKSNLAGKPVICATQMLESMTYNPRPTRAEVSDVGNAILDGADCVMLSGETAKGNYPINAVTTMAETAVIAEQAIAYLPNYDDMRNCTPKPTSTTETVAASAVAAVFEQKAKAIIVLSTSGTTPRLVSKYRPNCPIILVTRCPRAARFSHLYRGVFPFVFEKE-----TDDVEARINFGIEKAKEFGILKKGDTYVSIQG--------NTLQVSTV 500
                                    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      |  -  |    460       470       480   |     -  |    500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        447   453                            484      493

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Pyruvate Kinase; Chain: A, domain 1 (36)

Homologous Superfamily: [code=3.40.1380.20, no name defined] (20)

Baker's yeast (Saccharomyces cerevisiae) (2)

1a	1a3xA01	A:1-18,A:356-500
1b	1a3xB01	B:1-18,B:356-498

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Phosphoenolpyruvate-binding domains (67)

Baker's yeast (Saccharomyces cerevisiae) (2)

2a	1a3xA02	A:19-87,A:190-355
2b	1a3xB02	B:19-87,B:190-355

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: M1 Pyruvate Kinase; Domain 3 (24)

Homologous Superfamily: M1 Pyruvate Kinase; Domain 3 (20)

Baker's yeast (Saccharomyces cerevisiae) (2)

3a	1a3xA03	A:88-189
3b	1a3xB03	B:88-189

(no "Pfam Domain" information available for 1A3X)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KPYK1_YEAST | P00549)

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: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:0030955	potassium ion binding	Interacting selectively and non-covalently with potassium (K+) ions.
	GO:0004743	pyruvate kinase activity	Catalysis of the reaction: ATP + pyruvate = ADP + 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.
biological process
	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: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.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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(no "Related Entries Specified in the PDB File" available for 1A3X)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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