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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BETA ENOLASE ENOB
 
Authors :  M. Vollmar, E. Krysztofinska, A. Chaikuad, T. Krojer, R. Cocking, F. Vo C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, W. W. Yue, U. Oppe
Date :  30 Sep 10  (Deposition) - 10 Nov 10  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vollmar, E. Krysztofinska, A. Chaikuad, T. Krojer, R. Cocking, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, W. W. Yue, U. Oppermann
Crystal Structure Of Human Beta Enolase Enob
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-ENOLASE
    Chains: A, B
    EC Number: 4.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE, MUSCLE-SPECIFIC ENOLASE, MSE, SKELETAL MUSCLE ENOLASE, ENOLASE 3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric/Biological Unit (3, 23)
No.NameCountTypeFull Name
1EDO19Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:245 , GLU A:293 , ASP A:318 , HOH A:2267 , HOH A:2358 , HOH A:2506BINDING SITE FOR RESIDUE MG A 500
02AC2SOFTWAREGLU A:210 , LYS A:343 , ARG A:372 , SER A:373 , HOH A:2506 , HOH A:2542 , HOH A:2543BINDING SITE FOR RESIDUE PO4 A 501
03AC3SOFTWARELYS A:193 , THR A:205 , VAL A:207 , HOH A:2544 , ASP B:209BINDING SITE FOR RESIDUE EDO A 502
04AC4SOFTWARELYS A:202 , ASP A:203 , ALA A:204 , THR A:205 , ASN A:206 , GLY B:160 , HOH B:2301BINDING SITE FOR RESIDUE EDO A 503
05AC5SOFTWAREGLU A:219 , ASN A:220 , ASN A:221 , HOH A:2545BINDING SITE FOR RESIDUE EDO A 504
06AC6SOFTWAREGLY A:273 , GLU A:274 , GLY A:277 , PHE A:296 , THR A:303 , SER A:306 , PHE A:307 , HOH A:2396 , HOH A:2546BINDING SITE FOR RESIDUE EDO A 505
07AC7SOFTWAREGLU A:180 , ARG A:183 , ILE A:184 , TYR A:236 , HOH A:2547BINDING SITE FOR RESIDUE EDO A 506
08AC8SOFTWARELYS A:202 , GLY A:310 , VAL A:311 , ASN A:312 , EDO A:508 , HOH A:2548 , PHE B:261 , LYS B:262BINDING SITE FOR RESIDUE EDO A 507
09AC9SOFTWARELYS A:202 , VAL A:311 , ASN A:312 , EDO A:507 , HOH A:2549 , HOH A:2550 , LYS B:262 , SER B:263 , PRO B:264BINDING SITE FOR RESIDUE EDO A 508
10BC1SOFTWAREALA A:302 , HOH A:2288 , HOH A:2553 , HOH A:2554 , HOH A:2555 , LEU B:58BINDING SITE FOR RESIDUE EDO A 509
11BC2SOFTWAREASN A:338 , HOH A:2462 , HOH A:2556 , HOH A:2557BINDING SITE FOR RESIDUE EDO A 510
12BC3SOFTWAREGLU A:21 , ARG A:32 , ASP A:378 , HOH A:2558BINDING SITE FOR RESIDUE EDO A 511
13BC4SOFTWAREASP B:245 , GLU B:293 , ASP B:318 , HOH B:2254 , HOH B:2336 , HOH B:2514BINDING SITE FOR RESIDUE MG B 500
14BC5SOFTWAREGLU B:210 , LYS B:343 , ARG B:372 , SER B:373 , HOH B:2514BINDING SITE FOR RESIDUE PO4 B 501
15BC6SOFTWAREGLY A:160 , HOH A:2318 , LYS B:202 , ASP B:203 , ALA B:204 , THR B:205 , ASN B:206BINDING SITE FOR RESIDUE EDO B 502
16BC7SOFTWAREGLU B:219 , ASN B:220 , ASN B:221 , HOH B:2515BINDING SITE FOR RESIDUE EDO B 503
17BC8SOFTWAREHIS B:191 , GLY B:194 , VAL B:195 , EDO B:510 , HOH B:2516 , HOH B:2517 , HOH B:2518BINDING SITE FOR RESIDUE EDO B 504
18BC9SOFTWAREGLU A:10 , HOH A:2015 , HOH A:2017 , LYS B:179 , GLU B:415 , HOH B:2264BINDING SITE FOR RESIDUE EDO B 505
19CC1SOFTWAREASP A:209 , LYS B:193 , THR B:205 , ASN B:206 , HOH B:2519BINDING SITE FOR RESIDUE EDO B 506
20CC2SOFTWAREASP B:142 , LEU B:143 , ILE B:144 , ILE B:422 , HOH B:2492 , HOH B:2520 , HOH B:2521BINDING SITE FOR RESIDUE EDO B 507
21CC3SOFTWAREGLU B:274 , PHE B:307 , HOH B:2522BINDING SITE FOR RESIDUE EDO B 508
22CC4SOFTWAREGLU B:180 , ARG B:183 , TYR B:236 , HOH B:2334 , HOH B:2523BINDING SITE FOR RESIDUE EDO B 509
23CC5SOFTWARELEU A:58 , GLY B:194 , EDO B:504BINDING SITE FOR RESIDUE EDO B 510

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XSX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020618N71SENOB_HUMANPolymorphism238238A/BS71S
2UniProtVAR_020619V85AENOB_HUMANPolymorphism238239A/BA85A
3UniProtVAR_020620G156DENOB_HUMANDisease (GSD13)121918403A/BG156D
4UniProtVAR_020621G374EENOB_HUMANDisease (GSD13)121918404A/BG374E
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENOLASEPS00164 Enolase signature.ENOB_HUMAN340-353
 		  2A:340-353
B:340-353

(-) Exons   (0, 0)

(no "Exon" information available for 2XSX)

(-) Sequences/Alignments

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:434
 aligned with ENOB_HUMAN | P13929 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:434
                                    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    
           ENOB_HUMAN     1 MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKGRYLGKGVLKAVENINNTLGPALLQKKLSVVDQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGNPDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEALGDKAIFAGRKFRNPKAK 434
               SCOP domains d2xsxa1 A:1-140 automated matches                                                                                                           d2xsxa2 A:141-434 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......ee.eeeee.hhhh.......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.....eeeee.hhhh.ee..ee........hhhhh.hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------S-------------A----------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       --------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xsx A   1 MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKGRYLGKGVLKAVENINSTLGPALLQKKLSVADQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGNPDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEALGDKAIFAGRKFRNPKAK 434
                                    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:435
 aligned with ENOB_HUMAN | P13929 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:435
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429     
           ENOB_HUMAN     - -MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKGRYLGKGVLKAVENINNTLGPALLQKKLSVVDQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGNPDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEALGDKAIFAGRKFRNPKAK 434
               SCOP domains d2xsxb1 B:0-140 automated matches                                                                                                            d2xsxb2 B:141-434 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Enolase_N-2xsxB01 B:2-134                                                                                                            -------Enolase_C-2xsxB03 B:142-432                                                                                                                                                                                                                                                                        -- Pfam domains (1)
           Pfam domains (2) --Enolase_N-2xsxB02 B:2-134                                                                                                            -------Enolase_C-2xsxB04 B:142-432                                                                                                                                                                                                                                                                        -- Pfam domains (2)
         Sec.struct. author .....eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeeeeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.....eeeee.hhhh.ee..ee........hhhhh.hhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------S-------------A----------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xsx B   0 SMAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKGRYLGKGVLKAVENINSTLGPALLQKKLSVADQEKVDKFMIELDGTENKSKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGNPDLILPVPAFNVINGGSHAGNKLAMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDEGGFAPNILENNEALELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELYKSFIKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLKVNQIGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLMRIEEALGDKAIFAGRKFRNPKAK 434
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ENOB_HUMAN | P13929)
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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0061621    canonical glycolysis    The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
    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:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0043403    skeletal muscle tissue regeneration    The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  ENOB_HUMAN | P13929
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