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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-HYDROXYPENTADIENOIC ACID HYDRATASE FROM ESCHERICHIA COLI
 
Authors :  A. A. Fedorov, E. V. Fedorov, A. Sharp, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  28 Mar 04  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Hydratase, Structural Genomics, Nysgxrc Target T795, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, A. Sharp, S. C. Almo
Crystal Structure Of 2-Hydroxypentadienoic Acid Hydratase From Escherichia Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-KETO-4-PENTENOATE HYDRATASE
    Chains: A, B, C, D, E
    EC Number: 4.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MHPD, B0350
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 2-HYDROXYPENTADIENOIC ACID HYDRATASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1SV6)

(-) Sites  (0, 0)

(no "Site" information available for 1SV6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SV6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SV6)

(-) Exons   (0, 0)

(no "Exon" information available for 1SV6)

(-) 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:261
 aligned with MHPD_ECOLI | P77608 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:261
                                    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 
           MHPD_ECOLI     1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
               SCOP domains d1sv6a_ A: 2-keto-4-pentenoate hydratase MhpD                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sv6A00 A:1-261 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhh......eeeeee...eee..eee........eeeeeeeeee.........hhhhhhh.eeeeeeeeeee.........hhhhhhhh...eeeeee...............eeeeee..eeeeeee.hhh..hhhhhhhhhhhhhhhh........eeeeee....ee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sv6 A   1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
                                    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 


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with MHPD_ECOLI | P77608 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:261
                                    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 
           MHPD_ECOLI     1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
               SCOP domains d1sv6b_ B: 2-keto-4-pentenoate hydratase MhpD                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sv6B00 B:1-261 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhh......eeeeee...eee..eee........eeeeeeeeee.........hhhhhhh.eeeeeeeeeee.........hhhhhhhh...eeeeee...............eeeeee..eeeeeee.hhh..hhhhhhhhhhhhhhhh........eeeeee....ee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sv6 B   1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
                                    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 


Chain C from PDB  Type:PROTEIN  Length:261
 aligned with MHPD_ECOLI | P77608 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:261
                                    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 
           MHPD_ECOLI     1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
               SCOP domains d1sv6c_ C: 2-keto-4-pentenoate hydratase MhpD                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sv6C00 C:1-261 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhh......eeeeee...eee..eee........eeeeeeeeee.........hhhhhhh.eeeeeeeeeee.........hhhhhhhh...eeeeee...............eeeeee..eeeeeee.hhh..hhhhhhhhhhhhhhhh........eeeeee....ee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sv6 C   1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
                                    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 


Chain D from PDB  Type:PROTEIN  Length:261
 aligned with MHPD_ECOLI | P77608 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:261
                                    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 
           MHPD_ECOLI     1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
               SCOP domains d1sv6d_ D: 2-keto-4-pentenoate hydratase MhpD                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sv6D00 D:1-261 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhh......eeeeee...eee..eee........eeeeeeeeee.........hhhhhhh.eeeeeeeeeee.........hhhhhhhh...eeeeee...............eeeeee..eeeeeee.hhh..hhhhhhhhhhhhhhhh........eeeeee....ee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sv6 D   1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
                                    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 


Chain E from PDB  Type:PROTEIN  Length:261
 aligned with MHPD_ECOLI | P77608 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:261
                                    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 
           MHPD_ECOLI     1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
               SCOP domains d1sv6e_ E: 2-keto-4-pentenoate hydratase MhpD                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sv6E00 E:1-261 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ------------------------------------------------------FAA_hydrolase-1sv6E01 E:55-260                                                                                                                                                                                - Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------FAA_hydrolase-1sv6E02 E:55-260                                                                                                                                                                                - Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------FAA_hydrolase-1sv6E03 E:55-260                                                                                                                                                                                - Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------FAA_hydrolase-1sv6E04 E:55-260                                                                                                                                                                                - Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------FAA_hydrolase-1sv6E05 E:55-260                                                                                                                                                                                - Pfam domains (5)
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhh......eeeeee...eee..eee........eeeeeeeeee.........hhhhhhh.eeeeeeeeeee.........hhhhhhhh...eeeeee...............eeeeee..eeeeeee.hhh..hhhhhhhhhhhhhhhh........eeeeee....ee.....eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sv6 E   1 MTKHTLEQLAADLRRAAEQGEAIAPLRDLIGIDNAEAAYAIQHINVQHDVAQGRRVVGRKVGLTHPKVQQQLGVDQPDFGTLFADMCYGDNEIIPFSRVLQPRIEAEIALVLNRDLPATDITFDELYNAIEWVLPALEVVGSRIRDWSIQFVDTVADNASCGVYVIGGPAQRPAGLDLKNCAMKMTRNNEEVSSGRGSECLGHPLNAAVWLARKMASLGEPLRTGDIILTGALGPMVAVNAGDRFEAHIEGIGSVAATFSS 261
                                    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
   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  (1, 5)

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

(-) CATH Domains  (1, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: FAH (11)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (MHPD_ECOLI | P77608)
molecular function
    GO:0008684    2-oxopent-4-enoate hydratase activity    Catalysis of the reaction: 4-hydroxy-2-oxopentanoate = 2-oxopent-4-enoate + H2O.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
biological process
    GO:0019380    3-phenylpropionate catabolic process    The chemical reactions and pathways resulting in the breakdown of 3-phenylpropionate, the anion of phenylpropanoic acid.
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1sv6
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 Related Entries

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

UniProtKB/Swiss-Prot
        MHPD_ECOLI | P77608: 2wqt

(-) Related Entries Specified in the PDB File

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