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Title :   ASYMMETRIC YEAST ENOLASE DIMER COMPLEXED WITH RESOLVED 2'-PHOSPHOGLYCERATE AND PHOSPHOENOLPYRUVATE

Authors :   L. Lebioda

Date :   08 Sep 97 (Deposition) - 14 Jan 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Lyase, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Zhang, J. M. Brewer, W. Minor, L. A. Carreira, L. Lebioda
Mechanism Of Enolase: The Crystal Structure Of Asymmetric Dimer Enolase-2-Phospho-D-Glycerate/Enolase- Phosphoenolpyruvate At 2. 0 A Resolution.
Biochemistry V. 36 12526 1997
PubMed-ID: 9376357 | Reference-DOI: 10.1021/BI9712450
(for further references see the PDB file header)

Molecule 1 - ENOLASE
	Chains	:	A, B
	EC Number	:	4.2.1.11
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	2-PHOSPHO-D-GLYCERATE HYDROLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	2PG	1	Ligand/Ion	2-PHOSPHOGLYCERIC ACID
2	LI	1	Ligand/Ion	LITHIUM ION
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	PEP	1	Ligand/Ion	PHOSPHOENOLPYRUVATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:246 , GLU A:295 , ASP A:320 , LYS A:396 , 2PG A:441 , HOH A:576	BINDING SITE FOR RESIDUE MG A 450
2	AC2	SOFTWARE	SER A:39 , ASP A:320 , LYS A:345 , 2PG A:441 , HOH A:568 , HOH A:604	BINDING SITE FOR RESIDUE LI A 451
3	AC3	SOFTWARE	ASP B:246 , GLU B:295 , ASP B:320 , PEP B:440 , HOH B:628	BINDING SITE FOR RESIDUE MG B 460
4	AC4	SOFTWARE	GLY A:37 , ALA A:38 , SER A:39 , HIS A:159 , GLN A:167 , GLU A:168 , GLU A:211 , ASP A:246 , GLU A:295 , ASP A:320 , LEU A:343 , LYS A:345 , HIS A:373 , ARG A:374 , SER A:375 , LYS A:396 , MG A:450 , LI A:451 , HOH A:568 , HOH A:604	BINDING SITE FOR RESIDUE 2PG A 441
5	AC5	SOFTWARE	GLY B:37 , ALA B:38 , SER B:39 , THR B:40 , ASP B:246 , GLU B:295 , ASP B:320 , LEU B:343 , LYS B:345 , HIS B:373 , ARG B:374 , SER B:375 , LYS B:396 , MG B:460 , HOH B:867	BINDING SITE FOR RESIDUE PEP B 440

(no "SS Bond" information available for 2ONE)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:142	-	Pro A:143
2	Ser B:142	-	Pro B:143
3	Asn B:264	-	Pro B:265

(no "SAP(SNP)/Variant" information available for 2ONE)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOLASE	PS00164	Enolase signature.	ENO1_YEAST	343-356	2	A:342-355 B:342-355

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YGR254W	1	YGR254W.1	VII:1000932-1002245	1314	ENO1_YEAST	1-437	437	2	A:1-436 B:1-436	436 436

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:436
 aligned with ENO1_YEAST | P00924 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:436
                                    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      
           ENO1_YEAST     2 AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL 437
               SCOP domains d2onea2 A:1-141 Enolase                                                                                                                      d2onea1 A:142-436 Enolase                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2oneA01 A:1-126 Enolase-like, N-terminal domain                                                                               2oneA02 A:127-436 Enolase superfamily                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeee..eeeeee.....................hhhh...hhhhhhhhh.hhhhhhhh......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh....hhhhhhhh.......eee.eeeeeeee.hhh........eeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhhh..............hhhhhhhhhhhhhh.......eeeee..hhhh......................hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhh..eee........hhhhhhhhhh....eeee.hhhh..hhhhhhhhhhhhh...eeee..........hhhhhhhh....eee......hhhhhhhhhhhhhhhhhhhheee.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       --------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-436 UniProt: 1-437 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 2one A   1 AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKVKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL 436
                                    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

Chain B from PDB  Type:PROTEIN  Length:436
 aligned with ENO1_YEAST | P00924 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:436
                                    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      
           ENO1_YEAST     2 AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL 437
               SCOP domains d2oneb2 B:1-141 Enolase                                                                                                                      d2oneb1 B:142-436 Enolase                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2oneB01 B:1-126 Enolase-like, N-terminal domain                                                                               2oneB02 B:127-436 Enolase superfamily                                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) Enolase_N-2oneB01 B:1-133                                                                                                            ---------Enolase_C-2oneB03 B:143-434                                                                                                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) Enolase_N-2oneB02 B:1-133                                                                                                            ---------Enolase_C-2oneB04 B:143-434                                                                                                                                                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author ...eeeeeeee.....eeeeeeeee..eeeeee......................hhh...hhhhhhhhh.hhhhhhhh......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...hhhhhhhhh......eee.eeeeeeee............eeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhhh..............hhhhhhhhhhhhhhh......eeeee..hhhh......................hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhh..eee........hhhhhhhhh.....eeee.hhhh..hhhhhhhhhhhhh...eeee..........hhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhheee.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       --------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-436 UniProt: 1-437 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 2one B   1 AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGASTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKVKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADDLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKL 436
                                    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

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) (23004)

Fold: Enolase N-terminal domain-like (211)

Superfamily: Enolase N-terminal domain-like (211)

Family: Enolase N-terminal domain-like (88)

Protein domain: Enolase (39)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (16)

1a	d2onea2	A:1-141
1b	d2oneb2	B:1-141

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Enolase C-terminal domain-like (212)

Family: Enolase (45)

Protein domain: Enolase (39)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (16)

2a	d2onea1	A:142-436
2b	d2oneb1	B:142-436

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: Enolase-like, N-terminal domain (130)

Baker's yeast (Saccharomyces cerevisiae) (16)

1a	2oneA01	A:1-126
1b	2oneB01	B:1-126

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Enolase superfamily (142)

Baker's yeast (Saccharomyces cerevisiae) (16)

2a	2oneA02	A:127-436
2b	2oneB02	B:127-436

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Enolase_N (69)

Family: Enolase_N (20)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (11)

1a	Enolase_N-2oneB01	B:1-133
1b	Enolase_N-2oneB02	B:1-133

Clan: Enolase_TIM (82)

Family: Enolase_C (20)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (11)

2a	Enolase_C-2oneB03	B:143-434
2b	Enolase_C-2oneB04	B:143-434

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ENO1_YEAST | P00924)

molecular function
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0004634	phosphopyruvate hydratase activity	Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	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:0032889	regulation of vacuole fusion, non-autophagic	Any process that modulates the frequency, rate or extent of the fusion of two vacuole membranes to form a single vacuole.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000324	fungal-type vacuole	A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0000015	phosphopyruvate hydratase complex	A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.

Asymmetric/Biological Unit
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