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Asym./Biol. Unit (Jmol Viewer)

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

Title :   ENGINEERING THE ENOLASE ACTIVE SITE POCKET: CRYSTAL STRUCTURE OF THE S39N D321R MUTANT OF YEAST ENOLASE 1

Authors :   B. Schreier, B. Hocker

Date :   08 Jun 10 (Deposition) - 25 Aug 10 (Release) - 20 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Lyase, Tim-Barrel, Glycolysis, Gluconeogenesis, Metal Binding, Enolase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Schreier, B. Hoecker
Engineering The Enolase Magnesium Ii Binding Site - Implications For Its Evolution.
Biochemistry V. 49 7582 2010
PubMed-ID: 20690637 | Reference-DOI: 10.1021/BI100954F

Molecule 1 - ENOLASE 1
	Chains	:	A, B
	EC Number	:	4.2.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 2-437
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	2-PHOSPHOGLYCERATE DEHYDRATASE, 1,2-PHOSPHO-D-GLYCERATE HYDRO-LYASE 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	MG	5	Ligand/Ion	MAGNESIUM ION
2	PEP	2	Ligand/Ion	PHOSPHOENOLPYRUVATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:246 , GLU A:295 , ASP A:320 , LYS A:396 , PEP A:1440 , HOH A:2298	BINDING SITE FOR RESIDUE MG A1439
2	AC2	SOFTWARE	GLY A:37 , ALA A:38 , GLU A:168 , GLU A:211 , ASP A:246 , GLU A:295 , ASP A:320 , ARG A:321 , LEU A:343 , LYS A:345 , ARG A:374 , SER A:375 , LYS A:396 , MG A:1439 , HOH A:2233 , HOH A:2407	BINDING SITE FOR RESIDUE PEP A1440
3	AC3	SOFTWARE	ASP A:135 , HOH A:2195 , HOH A:2201 , HOH A:2202 , HOH A:2213 , HOH B:2272	BINDING SITE FOR RESIDUE MG A1441
4	AC4	SOFTWARE	HOH A:2062 , HOH A:2109 , HOH A:2110 , HOH A:2163 , HOH B:2298	BINDING SITE FOR RESIDUE MG A1442
5	AC5	SOFTWARE	ASP B:246 , GLU B:295 , ASP B:320 , PEP B:1440 , HOH B:2293 , HOH B:2392	BINDING SITE FOR RESIDUE MG B1439
6	AC6	SOFTWARE	GLN B:167 , GLU B:168 , ASP B:246 , GLU B:295 , ASP B:320 , LYS B:345 , SER B:372 , SER B:375 , LYS B:396 , MG B:1439 , HOH B:2392 , HOH B:2393	BINDING SITE FOR RESIDUE PEP B1440
7	AC7	SOFTWARE	HOH A:2263 , ASP B:135 , HOH B:2090 , HOH B:2193 , HOH B:2194 , HOH B:2208	BINDING SITE FOR RESIDUE MG B1441

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

Asymmetric/Biological Unit

No.	Residues
1	Ser A:142	-	Pro A:143
2	Ser B:142	-	Pro B:143

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

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)
	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:438
 aligned with ENO1_YEAST | P00924 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             437  
                                    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--   -
               SCOP domains d2xgza1 A:1-140 automated matches                                                                                                           d2xgza2 A:141-438 automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eee.eeeeeeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.....eeeee.hhhh.ee..ee.........hhhhh.hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh.eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhh.. 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
                 2xgz A   1 AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGANTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADRLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKLLH 438
                                    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:438
 aligned with ENO1_YEAST | P00924 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             437  
                                    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--   -
               SCOP domains d2xgzb1 B:1-140 automated matches                                                                                                           d2xgzb2 B:141-438 automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Enolase_N-2xgzB01 B:1-133                                                                                                            ---------Enolase_C-2xgzB03 B:143-434                                                                                                                                                                                                                                                                         ---- Pfam domains (1)
           Pfam domains (2) Enolase_N-2xgzB02 B:1-133                                                                                                            ---------Enolase_C-2xgzB04 B:143-434                                                                                                                                                                                                                                                                         ---- Pfam domains (2)
         Sec.struct. author ...eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....eee.ee.eeeee.hhhh.......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.....eeeee.hhhh.ee..ee...............hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh.eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhh.. 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
                 2xgz B   1 AVSKVYARSVYDSRGNPTVEVELTTEKGVFRSIVPSGANTGVHEALEMRDGDKSKWMGKGVLHAVKNVNDVIAPAFVKANIDVKDQKAVDDFLISLDGTANKSKLGANAILGVSLAASRAAAAEKNVPLYKHLADLSKSKTSPYVLPVPFLNVLNGGSHAGGALALQEFMIAPTGAKTFAEALRIGSEVYHNLKSLTKKRYGASAGNVGDEGGVAPNIQTAEEALDLIVDAIKAAGHDGKIKIGLDCASSEFFKDGKYDLDFKNPNSDKSKWLTGPQLADLYHSLMKRYPIVSIEDPFAEDDWEAWSHFFKTAGIQIVADRLTVTNPKRIATAIEKKAADALLLKVNQIGTLSESIKAAQDSFAAGWGVMVSHRSGETEDTFIADLVVGLRTGQIKTGAPARSERLAKLNQLLRIEEELGDNAVFAGENFHHGDKLLH 438
                                    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 '\|'

(no "CATH Domain" information available for 2XGZ)

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-2xgzB01	B:1-133
1b	Enolase_N-2xgzB02	B:1-133

Clan: Enolase_TIM (82)

Family: Enolase_C (20)

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

2a	Enolase_C-2xgzB03	B:143-434
2b	Enolase_C-2xgzB04	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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	Cis Peptide Bonds
		Ser A:142 - Pro A:143	[ RasMol ]
		Ser B:142 - Pro B:143	[ RasMol ]

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	2xgz
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	4.2.1.11
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1ebg	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) (APO FORM)
1ebh	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) COMPLEXED WITH MG 2+
1els	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) COMPLEXED WITH PHOSPHONOACETOHYDROXAMATE AND MANGANESE
1l8p	MG-PHOSPHONOACETOHYDROXAMATE COMPLEX OF S39A YEAST ENOLASE 1
1nel	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) COMPLEX WITH ORTHOPHOSPHATE, FLUORIDE AND MAGNESIUM
1one	YEAST ENOLASE COMPLEXED WITH AN EQUILIBRIUM MIXTURE OF 2'-PHOSPHOGLYCEATE AND PHOSPHOENOLPYRUVATE
1p43	REVERSE PROTONATION IS THE KEY TO GENERAL ACID-BASECATALYSIS IN ENOLASE
1p48	REVERSE PROTONATION IS THE KEY TO GENERAL ACID-BASECATALYSIS IN ENOLASE
2al1	CRYSTAL STRUCTURE ANALYSIS OF ENOLASE MG SUBUNIT COMPLEX AT PH 8.0
2al2	CRYSTAL STRUCTURE ANALYSIS OF ENOLASE MG SUBUNIT COMPLEX AT PH 8.0
2one	ASYMMETRIC YEAST ENOLASE DIMER COMPLEXED WITH RESOLVED 2'-PHOSPHOGLYCERATE AND PHOSPHOENOLPYRUVATE
2xh0	ENGINEERING THE ENOLASE ACTIVE SITE POCKET: CRYSTAL STRUCTURE OF THE S39N Q167K D321R MUTANT OF YEAST ENOLASE 1
2xh2	ENGINEERING THE ENOLASE ACTIVE SITE POCKET: CRYSTAL STRUCTURE OF THE S39N D321A MUTANT OF YEAST ENOLASE 1
2xh4	ENGINEERING THE ENOLASE ACTIVE SITE POCKET: CRYSTAL STRUCTURE OF THE S39A D321A MUTANT OF YEAST ENOLASE 1
2xh7	ENGINEERING THE ENOLASE ACTIVE SITE POCKET: CRYSTAL STRUCTURE OF THE D321A MUTANT OF YEAST ENOLASE 1
3enl	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) (APO)
4enl	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) (HOLO)
5enl	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) COMPLEX WITH 2-PHOSPHO-D-GLYCERIC ACID AND CALCIUM
6enl	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) COMPLEX WITH PHOSPHOGLYCOLIC ACID AND ZINC
7enl	ENOLASE (2-PHOSPHO-D-GLYCERATE HYDROLASE) COMPLEX WITH 2-PHOSPHO-D-GLYCERIC ACID AND MAGNESIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (12, 12)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File