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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HPCE FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Mar 05  (Deposition) - 21 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Hpce, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of The Hpce From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HPCE
    Chains: A, B, C, D
    EC Number: 5.3.3.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:97 , GLU A:99 , ASP A:128 , LYS A:146 , HOH A:1012 , HOH A:1030BINDING SITE FOR RESIDUE NA A 1007
2AC2SOFTWAREARG C:140 , ALA D:50 , LEU D:51 , ARG D:140 , PRO D:141 , HOH D:1189 , HOH D:1210 , HOH D:1214BINDING SITE FOR RESIDUE SO4 D 1008
3AC3SOFTWAREVAL A:120 , LEU A:121 , VAL A:160 , GLU A:161 , VAL A:163 , HOH A:1024 , HOH A:1143BINDING SITE FOR RESIDUE GOL A 1001
4AC4SOFTWARETRP A:37 , HIS A:81 , PHE A:157 , GLY A:236 , ALA A:237BINDING SITE FOR RESIDUE GOL A 1002
5AC5SOFTWARETRP B:37 , HIS B:81 , PHE B:157 , GLY B:236 , ALA B:237 , HOH B:1200 , HOH B:1202BINDING SITE FOR RESIDUE GOL B 1003
6AC6SOFTWAREVAL B:120 , LEU B:121 , GLY B:122 , TYR B:123 , VAL B:160 , GLU B:161 , VAL B:163 , HOH B:1040 , HOH B:1114BINDING SITE FOR RESIDUE GOL B 1004
7AC7SOFTWARETYR C:17 , TRP C:37 , HIS C:81 , PHE C:157 , GLY C:236 , ALA C:237BINDING SITE FOR RESIDUE GOL C 1005
8AC8SOFTWARETYR D:17 , TRP D:37 , HIS D:81 , PHE D:157 , GLY D:236 , ALA D:237BINDING SITE FOR RESIDUE GOL D 1006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:155 -Pro A:156
2Arg B:140 -Pro B:141
3Gly B:155 -Pro B:156
4Gly C:155 -Pro C:156
5Arg D:140 -Pro D:141
6Gly D:155 -Pro D:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WZO)

(-) 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:236
 aligned with Q5SJQ0_THET8 | Q5SJQ0 from UniProtKB/TrEMBL  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q5SJQ0_THET8     1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYADHAEELGLSRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEEP 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ----------------------------------------1wzoA02 A:41-2      46 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee..eee.....eehhhhhee........eeeee....------........eeeeehhh.ee.....eee......ee..eeeeeee.......hhhhhh..eeeeeeee..ee.hhh----..hhhhhh....eeeeeeee..........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee........ee....eeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wzo A   1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYA------GLSRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYV----RPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEEP 246
                                    10        20        30        40        50   |     -|       70        80        90       100       110       120       130    |  140       150       160       170       180       190       200       210       220       230       240      
                                                                                54     61                                                                       135  140                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q5SJQ0_THET8 | Q5SJQ0 from UniProtKB/TrEMBL  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q5SJQ0_THET8     1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYADHAEELGLSRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEEP 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ----------------------------------------1wzoB02 B:41-2        46 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee..eee.....eehhhhhee........eeeee....--------......eeeeehhh.ee.....eee......ee..eeeeeee.......hhhhhh..eeeeeeee..ee.hhh......hhhhhh....eeeeeeee..........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee........ee....eeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wzo B   1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYA--------SRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEEP 246
                                    10        20        30        40        50   |     -  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
                                                                                54       63                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:236
 aligned with Q5SJQ0_THET8 | Q5SJQ0 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
         Q5SJQ0_THET8     1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYADHAEELGLSRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEE 245
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------1wzoC02 C:41-2         45 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee..eee.....eehhhhhee........eeeee....---------.....eeeeehhh.ee.....eee......ee..eeeeeee.......hhhhhh..eeeeeeee..ee.hhh......hhhhhh....eeeeeeee..........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee..............eeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wzo C   1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYA---------RPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEE 245
                                    10        20        30        40        50   |     -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                                                                                54        64                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with Q5SJQ0_THET8 | Q5SJQ0 from UniProtKB/TrEMBL  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q5SJQ0_THET8     1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYADHAEELGLSRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEEP 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ----------------------------------------1wzoD02 D:41-2        46 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                               CATH domains
           Pfam domains (1) --------------------------------------------FAA_hydrol        ase-1wzoD01 D:45-243                                                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------FAA_hydrol        ase-1wzoD02 D:45-243                                                                                                                                                                 --- Pfam domains (2)
           Pfam domains (3) --------------------------------------------FAA_hydrol        ase-1wzoD03 D:45-243                                                                                                                                                                 --- Pfam domains (3)
           Pfam domains (4) --------------------------------------------FAA_hydrol        ase-1wzoD04 D:45-243                                                                                                                                                                 --- Pfam domains (4)
         Sec.struct. author .eeeeeee..eeeeeeee..eee.....eehhhhhee........eeeee....--------......eeee.hhh.ee.....eee......ee..eeeeeee.......hhhhhh..eeeeeeee..ee.hhh......hhhhhh....eeeeeeee..........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee........ee....eeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wzo D   1 MKLARFLAKGRVHQGVYREGLLLDEAGEAHRPEDVTWLLPFTPGKILGVALNYA--------SRPEEPALFWKPNTSLLPHKGVVLYPKGARFVHYEVELAVVVGRPMKRVRAKDALDYVLGYTIANDLVARDYVTNTFRPPIRAKGRDTFLPLGPFLVVEEVEDPQDLWLRAYVNGELRQEGHTSRMLYSVAELLEFISEFMTLEPYDVLLTGTPKGISQVRPGDVMRLEIEGLGALENPIEEEP 246
                                    10        20        30        40        50   |     -  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
                                                                                54       63
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 1WZO)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: FAH (11)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SJQ0_THET8 | Q5SJQ0)
molecular function
    GO:0008704    5-carboxymethyl-2-hydroxymuconate delta-isomerase activity    Catalysis of the reaction: 5-carboxymethyl-2-hydroxymuconate = 5-carboxy-2-oxohept-3-enedioate.
    GO:0018800    5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase activity    Catalysis of the reaction: 5-oxopent-3-ene-1,2,5-tricarboxylate = 2-oxohept-3-enedioate + CO2.
    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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:1901023    4-hydroxyphenylacetate catabolic process    The chemical reactions and pathways resulting in the breakdown of 4-hydroxyphenylacetate.
    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.

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