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(-) Description

Title :  CRYSTAL STRUCTURE OF THE T. BRUCEI ENOLASE COMPLEXED WITH FLUORO-PHOSPHONOACETOHYDROXAMATE (FPAH)
 
Authors :  M. V. A. S. Navarro, D. J. Rigden, R. C. Garratt, S. M. G. Dias
Date :  08 May 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lyase, Glycolysis, His-Tag (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Navarro, S. M. Gomes Dias, L. V. Mello, M. T. Da Silva Giotto, S. Gavalda, C. Blonski, R. C. Garratt, D. J. Rigden
Structural Flexibility In Trypanosoma Brucei Enolase Revealed By X-Ray Crystallography And Molecular Dynamics.
Febs J. V. 274 5077 2007
PubMed-ID: 17822439  |  Reference-DOI: 10.1111/J.1742-4658.2007.06027.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENOLASE
    Chains: A
    EC Number: 4.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synonym: 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FSG1Ligand/Ion[(1S)-1-FLUORO-2-(HYDROXYAMINO)-2-OXOETHYL]PHOSPHONICACID
3ZN3Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FSG2Ligand/Ion[(1S)-1-FLUORO-2-(HYDROXYAMINO)-2-OXOETHYL]PHOSPHONICACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:243 , GLU A:291 , ASP A:318 , FSG A:600 , HOH A:759BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWARESER A:40 , FSG A:600 , HOH A:727 , HOH A:817BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWAREHIS A:0 , GLU A:27 , HIS A:283 , HOH A:1042BINDING SITE FOR RESIDUE ZN A 550
4AC4SOFTWAREGLY A:38 , ALA A:39 , SER A:40 , GLN A:164 , GLU A:165 , GLU A:208 , ASP A:243 , GLU A:291 , ASP A:318 , LEU A:341 , LYS A:343 , ARG A:372 , SER A:373 , LYS A:394 , ZN A:500 , ZN A:501 , HOH A:722 , HOH A:727 , HOH A:760 , HOH A:817BINDING SITE FOR RESIDUE FSG A 600
5AC5SOFTWAREARG A:32 , TYR A:129 , GLN A:409 , GLU A:416 , HOH A:738 , HOH A:782BINDING SITE FOR RESIDUE EDO A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PU1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PU1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PU1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PU1)

(-) Exons   (0, 0)

(no "Exon" information available for 2PU1)

(-) Sequences/Alignments

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:431
 aligned with Q38BV6_TRYB2 | Q38BV6 from UniProtKB/TrEMBL  Length:429

    Alignment length:431
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428 
         Q38BV6_TRYB2     - --MTIQKVHGREVLDSRGNPTVEVEVTTERGVFRSAVPSGASTGVYEACELRDGDKKRYVGKGCLQAVKNVNEVIGPALIGRDELKQEELDTLMLRLDGTPNKGKLGANAILGCSMAISKAAAAAKGVPLYRYLASLAGTKELRLPVPCFNVINGGKHAGNALPFQEFMIAPVKATSFSEALRMGSEVYHSLRGIIKKKYGQDAVNVGDEGGFAPPIKDINEPLPILMEAIEEAGHRGKFAICMDCAASETYDEKKQQYNLTFKSPEPTWVTAEQLRETYCKWAHDYPIVSIEDPYDQDDFAGFAGITEALKGKTQIVGDDLTVTNTERIKMAIEKKACNSLLLKINQIGTISEAIASSKLCMENGWSVMVSHRSGETEDTYIADLVVALGSGQIKTGAPCRGERTAKLNQLLRIEEELGAHAKFGFPGWS 429
               SCOP domains d2pu1a2 A:-1-138 Enolase                                                                                                                    d2pu1a1 A:139-429 Enolase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Enolase_N-2pu1A01 A:2-132                                                                                                          -------Enolase_C-2pu1A02 A:140-426                                                                                                                                                                                                                                                                    --- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....ee.ee.eeeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh......eeeee.hhhh.ee....eee.........eehhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhh....eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhh...ee.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pu1 A  -1 SHMTIQKVHGREVLDSRGNPTVEVEVTTEKGVFRSAVPSGASTGVYEACELRDGDKKRYVGKGCLQAVKNVNEVIGPALIGRDELKQEELDTLMLRLDGTPNKGKLGANAILGCSMAISKAAAAAKGVPLYRYLASLAGTKELRLPVPCFNVINGGKHAGNALPFQEFMIAPVKATSFSEALRMGSEVYHSLRGIIKKKYGQDAVNVGDEGGFAPPIKDINEPLPILMEAIEEAGHRGKFAICMDCAASETYDEKKQQYNLTFKSPEPTWVTAEQLRETYCKWAHDYPIVSIEDPYDQDDFAGFAGITEALKGKTQIVGDDLTVTNTERIKMAIEKKACNSLLLKINQIGTISEAIASSKLCMENGWSVMVSHRSGETEDTYIADLVVALGSGQIKTGAPCRGERTAKLNQLLRIEEELGAHAKFGFPGWS 429
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428 


Chain A from PDB  Type:PROTEIN  Length:431
 aligned with Q9NDH8_TRYBB | Q9NDH8 from UniProtKB/TrEMBL  Length:429

    Alignment length:431
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428 
         Q9NDH8_TRYBB     - --MTIQKVHGREVLDSRGNPTVEVEVTTERGVFRSAVPSGASTGVYEACELRDGDKKRYVGKGCLQAVKNVNEVIGPALIGRDELKQEELDTLMLRLDGTPNKGKLGANAILGCSMAISKAAAAAKGVPLYRYLASLAGTKELRLPVPCFNVINGGKHAGNALPFQEFMIAPVKATSFSEALRMGSEVYHSLRGIIKKKYGQDAVNVGDEGGFAPPIKDINEPLPILMEAIEEAGHRGKFAICMDCAASETYDEKKQQYNLTFKSPEPTWVTAEQLRETYCKWAHDYPIVSIEDPYDQDDFAGFAGITEALKGKTQIVGDDLTVTNTERIKMAIEKKACNSLLLKINQIGTISEAIASSKLCMENGWSVMVSHRSGETEDTYIADLVVALGSGQIKTGAPCRGERTAKLNQLLRIEEELGAHAKFGFPGWS 429
               SCOP domains d2pu1a2 A:-1-138 Enolase                                                                                                                    d2pu1a1 A:139-429 Enolase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Enolase_N-2pu1A01 A:2-132                                                                                                          -------Enolase_C-2pu1A02 A:140-426                                                                                                                                                                                                                                                                    --- Pfam domains
         Sec.struct. author ......eeeeeeee.....eeeeeeeee..eeeeee.....................hhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....ee.ee.eeeee............eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh......eeeee.hhhh.ee....eee.........eehhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhh....eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhh...ee.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pu1 A  -1 SHMTIQKVHGREVLDSRGNPTVEVEVTTEKGVFRSAVPSGASTGVYEACELRDGDKKRYVGKGCLQAVKNVNEVIGPALIGRDELKQEELDTLMLRLDGTPNKGKLGANAILGCSMAISKAAAAAKGVPLYRYLASLAGTKELRLPVPCFNVINGGKHAGNALPFQEFMIAPVKATSFSEALRMGSEVYHSLRGIIKKKYGQDAVNVGDEGGFAPPIKDINEPLPILMEAIEEAGHRGKFAICMDCAASETYDEKKQQYNLTFKSPEPTWVTAEQLRETYCKWAHDYPIVSIEDPYDQDDFAGFAGITEALKGKTQIVGDDLTVTNTERIKMAIEKKACNSLLLKINQIGTISEAIASSKLCMENGWSVMVSHRSGETEDTYIADLVVALGSGQIKTGAPCRGERTAKLNQLLRIEEELGAHAKFGFPGWS 429
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric 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 2PU1)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9NDH8_TRYBB | Q9NDH8)
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.
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.
cellular component
    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.

Chain A   (Q38BV6_TRYB2 | Q38BV6)
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.
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.
cellular component
    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.

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  2pu1
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  Q9NDH8_TRYBB | Q9NDH8
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q38BV6_TRYB2 | Q38BV6: 2ptw 2ptx 2pty 2ptz 2pu0
        Q9NDH8_TRYBB | Q9NDH8: 1oep

(-) Related Entries Specified in the PDB File

1oep FIRST STRUCTURE OF THE T. BRUCEI ENOLASE
2ptw THE SAME PROTEIN COMPLEXED WITH SULPHATE AND ZN ION IN A METAL BINDING SITE IV
2ptx CLOSED CONFORMATION OF THE T. BRUCEI ENOLASE COMPLEXED WITH SULPHATE
2pty THE SAME PROTEIN COMPLEXED WITH PEP
2ptz THE SAME PROTEIN COMPLEXED WITH PAH, HIS156-OUT CONFORMATION
2pu0 THE SAME PROTEIN COMPLEXED WITH PAH, HIS156-IN CONFORMATION