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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Mar 06  (Deposition) - 03 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  2-Hydroxyhepta-2, 4-Diene-1, 7-Dioate Isomerase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of The 2-Hydroxyhepta-2, 4-Diene-1, 7-Dioat Isomerase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DFU)

(-) Sites  (0, 0)

(no "Site" information available for 2DFU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:171 -Pro A:172
2Gly B:171 -Pro B:172
3Gly C:171 -Pro C:172
4Gly D:171 -Pro D:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DFU)

(-) 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:251
 aligned with Q5SK43_THET8 | Q5SK43 from UniProtKB/TrEMBL  Length:264

    Alignment length:264
                                    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    
         Q5SK43_THET8     1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNYREHIREMGHDFGEDLPKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------2dfuA02 A:45-2             64 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeeee..eeeee......eeeeeee.hhh.ee.......eeee.....-------------......eeeehhh.ee......hhhhhh..eee......ee..eeeeeee.......hhhhhh..eeeeeeee..eehhhhhhh..hhhhhh....eeeeeeee........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee..............eeeeee...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dfu A   1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNYR-------------LPKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
                                    10        20        30        40        50       | -         - |      80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                    58            72                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q5SK43_THET8 | Q5SK43 from UniProtKB/TrEMBL  Length:264

    Alignment length:264
                                    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    
         Q5SK43_THET8     1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNYREHIREMGHDFGEDLPKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------2dfuB02 B:45-               264 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeeee..eeeee......eeeeeee.hhh.ee.......eeee....---------------.....eeeehhh.ee......hhhhhh..eee......ee..eeeeeee.......hhhhhh..eeeeeeee..eehhhhhhh..hhhhhh....eeeeeeee........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee..............eeeeee...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dfu B   1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNY---------------PKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
                                    10        20        30        40        50      |  -         -  |     80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                   57              73                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:249
 aligned with Q5SK43_THET8 | Q5SK43 from UniProtKB/TrEMBL  Length:264

    Alignment length:264
                                    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    
         Q5SK43_THET8     1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNYREHIREMGHDFGEDLPKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------2dfuC02 C:45-               264 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeeee..eeeee......eeeeeee.hhh.ee.......eeee....---------------.....eeeehhh.ee......hhhhhh..eee......eee.eeeeeee.......hhhhhh..eeeeeeee..ee.hhhhhh..hhhhhh....eeeeeeee........eeeeee..eeeeeee.hhh..hhhhhhhhhhhhh......eee.......ee.....eeeeee...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dfu C   1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNY---------------PKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
                                    10        20        30        40        50      |  -         -  |     80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                   57              73                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:247
 aligned with Q5SK43_THET8 | Q5SK43 from UniProtKB/TrEMBL  Length:264

    Alignment length:264
                                    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    
         Q5SK43_THET8     1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNYREHIREMGHDFGEDLPKEPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --------------------------------------------2dfuD02 D:45-                 264 Fumarylacetoacetate hydrolase, domain 2                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeeeee..eeeee......eeeeeee.hhh.ee.......eeeee...-----------------..eeeeehhh.ee..............eee......ee..eeeeeee.......hhhhhh..eeeeeeee..eehhhhhhh..hhhhhh....eeeeeeee........eeeeee..eeeeeee.hhh..hhhhhhhhhhh........eee..............eeeeee...eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dfu D   1 MKILRFNEGRWGVLEGELVLETDGPGGNPTGRRYDLASVTLLPPATPTKIVCVGRNY-----------------EPGLFLKGPNALARPGNPRDPWGTAEPVPYPFFTEELHYEGELAVVVGDRMRHVPPEKALDHVLGYTVAVDITARDVQKKDLQWVRAKSADKFLPLGPWLETDLNPQDTWVRTYVNGTLRQEGHTSQMIFSVAEILSYISTFMTLEPLDVVLTGTPEGVGALRPGDRLEVAVEGVGTLFTLIGPKEERPW 264
                                    10        20        30        40        50      |  -         -    |   80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
                                                                                   57                75
   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 2DFU)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DFU)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SK43_THET8 | Q5SK43)
molecular function
    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: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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    Gly A:171 - Pro A:172   [ RasMol ]  
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