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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-C BOND HYDROLASE MHPC
 
Authors :  M. G. Montgomery, G. Dunn, F. Mohammed, T. Robertson, J. -L. Garcia, A. Coker, T. D. H. Bugg, S. P. Wood
Date :  19 Jul 04  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Alpha/Beta Hydrolase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Dunn, M. G. Montgomery, F. Mohammed, A. Coker, J. B. Cooper, T. Robertson, J. -L. Garcia, T. D. H. Bugg, S. P. Wood
The Structure Of The C-C Bond Hydrolase Mhpc Provides Insights Into Its Catalytic Mechanism
J. Mol. Biol. V. 346 253 2005
PubMed-ID: 15663942  |  Reference-DOI: 10.1016/J.JMB.2004.11.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-HYDROXY-6-KETONONA-2,4-DIENEDIOIC ACID HYDROLASE
    Chains: A, B, C, D
    EC Number: 3.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PIPC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MHPC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 2-HYDROXY-6-KETO-NONA-2,4-DIENE-1,9-DIOIC ACID 5, 6-HYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY D:3041 , ALA D:3044 , ASN D:3049 , ARG D:3188BINDING SITE FOR RESIDUE CL D 1001
2AC2SOFTWAREGLY A:41 , ALA A:44 , ARG A:188BINDING SITE FOR RESIDUE CL A 1002
3AC3SOFTWAREHOH C:215 , GLY C:2041 , ALA C:2044 , ARG C:2188BINDING SITE FOR RESIDUE CL C 1003
4AC4SOFTWAREGLY B:1039 , GLY B:1041 , ASN B:1049BINDING SITE FOR RESIDUE CL B 1285

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U2E)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:146 -Pro A:147
2Met B:1146 -Pro B:1147
3Met C:2146 -Pro C:2147
4Met D:3146 -Pro D:3147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U2E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U2E)

(-) Exons   (0, 0)

(no "Exon" information available for 1U2E)

(-) 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:286
 aligned with MHPC_ECOLI | P77044 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:286
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
          MHPC_ECOLI      3 YQPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP  288
               SCOP domains d1u2ea_ A: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeee..eeeeeeeeee.....eeeee.......hhhhhh..hhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u2e A   -1 YQPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP  284
                                     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      


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with MHPC_ECOLI | P77044 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:286
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
          MHPC_ECOLI      3 YQPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP  288
               SCOP domains d1u2eb_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeee..eeeeeeeeee.....eeeee.......hhhhhhh.hhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u2e B  999 YQPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP 1284
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      


Chain C from PDB  Type:PROTEIN  Length:286
 aligned with MHPC_ECOLI | P77044 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:286
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
          MHPC_ECOLI      3 YQPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP  288
               SCOP domains d1u2ec_ C: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeee..eeeeeeeeee.....eeeee.......hhhhhhh.hhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u2e C 1999 YQPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP 2284
                                  2008      2018      2028      2038      2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208      2218      2228      2238      2248      2258      2268      2278      


Chain D from PDB  Type:PROTEIN  Length:285
 aligned with MHPC_ECOLI | P77044 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:285
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
          MHPC_ECOLI      4 QPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP  288
               SCOP domains d1u2ed_ D: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------Abhydrolase_6-1u2eD01 D:3039-3281                                                                                                                                                                                                                  --- Pfam domains (1)
           Pfam domains (2) ---------------------------------------Abhydrolase_6-1u2eD02 D:3039-3281                                                                                                                                                                                                                  --- Pfam domains (2)
           Pfam domains (3) ---------------------------------------Abhydrolase_6-1u2eD03 D:3039-3281                                                                                                                                                                                                                  --- Pfam domains (3)
           Pfam domains (4) ---------------------------------------Abhydrolase_6-1u2eD04 D:3039-3281                                                                                                                                                                                                                  --- Pfam domains (4)
         Sec.struct. author ...hhhhheeeeeeee..eeeeeeeeee.....eeeee.......hhhhhhh.hhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee..............hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...eeeeee.......hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1u2e D 3000 QPQTEAATSRFLNVEEAGKTLRIHFNDCGQGDETVVLLHGSGPGATGWANFSRNIDPLVEAGYRVILLDCPGWGKSDSVVNSGSRSDLNARILKSVVDQLDIAKIHLLGNSMGGHSSVAFTLKWPERVGKLVLMGGGTGGMSLFTPMPTEGIKRLNQLYRQPTIENLKLMMDIFVFDTSDLTDALFEARLNNMLSRRDHLENFVKSLEANPKQFPDFGPRLAEIKAQTLIVWGRNDRFVPMDAGLRLLSGIAGSELHIFRDCGHWAQWEHADAFNQLVLNFLARP 3284
                                  3009      3019      3029      3039      3049      3059      3069      3079      3089      3099      3109      3119      3129      3139      3149      3159      3169      3179      3189      3199      3209      3219      3229      3239      3249      3259      3269      3279
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1U2E)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MHPC_ECOLI | P77044)
molecular function
    GO:0052823    2-hydroxy-6-oxonona-2,4,7-trienedioate hydrolase activity    Catalysis of the reaction: (2E,4Z,7E)-2-hydroxy-6-oxonona-2,4,7-trienedioate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + fumarate + H+.
    GO:0018771    2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity    Catalysis of the reaction: (2E,4Z)-2-hydroxy-6-oxonona-2,4-dienedioate + H2O = (2E)-2-hydroxypenta-2,4-dienoate + H+ + succinate.
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019622    3-(3-hydroxy)phenylpropionate catabolic process    The chemical reactions and pathways resulting in the breakdown of 3-(3-hydroxy)phenylpropionate, a hydroxylated derivative of phenylpropionate.
    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.
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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  1u2e
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