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(-) Description

Title :  CRYSTAL STRUCTURE OF 2,6-DIHYDROXYBENZOATE DECARBOXYLASE COMPLEXED WITH INHIBITOR 2,3-DIHYDROXYBENZALDEHYDE
 
Authors :  M. Goto
Date :  01 Aug 06  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goto, H. Hayashi, I. Miyahara, K. Hirotsu, M. Yoshida, T. Oikawa
Crystal Structures Of Nonoxidative Zn-Dependent 2, 6-Dihydroxybenzoate (Gamma-Resorcylate) Decarboxylase Fro Rhizobium Sp. Strain Mtp-10005
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THERMOPHILIC REVERSIBLE GAMMA-RESORCYLATE DECARBOXYLASE
    Chains: A, B, C, D
    EC Number: 4.1.1.-
    Organism Scientific: RHIZOBIUM SP.
    Organism Taxid: 267998
    Strain: MTP-10005
    Synonym: 2,6-DIHYDROXYBENZOATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
123A4Ligand/Ion2,3-DIHYDROXYBENZALDEHYDE
2ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:8 , HIS A:10 , HIS A:164 , ASP A:287 , 23A A:1511BINDING SITE FOR RESIDUE ZN A 1501
2AC2SOFTWAREGLU B:8 , HIS B:10 , HIS B:164 , ASP B:287 , 23A B:1512BINDING SITE FOR RESIDUE ZN B 1502
3AC3SOFTWAREGLU C:8 , HIS C:10 , HIS C:164 , ASP C:287 , 23A C:1513BINDING SITE FOR RESIDUE ZN C 1503
4AC4SOFTWAREGLU D:8 , HIS D:10 , HIS D:164 , ASP D:287 , 23A D:1514BINDING SITE FOR RESIDUE ZN D 1504
5AC5SOFTWAREHIS A:10 , PHE A:23 , HIS A:164 , PRO A:185 , ASP A:287 , PHE A:290 , ZN A:1501 , HOH A:1576 , ASN B:234 , HOH B:1632BINDING SITE FOR RESIDUE 23A A 1511
6AC6SOFTWAREASN A:234 , HIS B:10 , PHE B:23 , HIS B:164 , PRO B:185 , ASP B:287 , PHE B:290 , ZN B:1502 , HOH B:1537 , HOH B:1688BINDING SITE FOR RESIDUE 23A B 1512
7AC7SOFTWAREHIS C:10 , HIS C:164 , PRO C:185 , ASP C:287 , PHE C:290 , ZN C:1503 , HOH C:1543 , HOH C:1686 , ASN D:234BINDING SITE FOR RESIDUE 23A C 1513
8AC8SOFTWAREASN C:234 , HOH C:1634 , HIS D:10 , HIS D:164 , PRO D:185 , ASP D:287 , PHE D:290 , ZN D:1504 , HOH D:1571BINDING SITE FOR RESIDUE 23A D 1514

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:61 -Pro A:62
2Trp A:288 -Pro A:289
3Ala B:61 -Pro B:62
4Trp B:288 -Pro B:289
5Ala C:61 -Pro C:62
6Trp C:288 -Pro C:289
7Ala D:61 -Pro D:62
8Trp D:288 -Pro D:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DVX)

(-) 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:325
 aligned with Q60GU1_9RHIZ | Q60GU1 from UniProtKB/TrEMBL  Length:327

    Alignment length:325
                                    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       270       280       290       300       310       320     
         Q60GU1_9RHIZ     1 MQGKVALEEHFAIPETLQDSAGFVPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKLD 325
               SCOP domains d2dvxa_ A: Thermophilic reversible gamma-resorcylate decarboxylase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.eeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee...............hhhhhhhhhhhhhhh..eeee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhh..............hhhhhhhhheeee.....hhhhhhhhhh..hhh.ee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvx A   1 MQGKVALEEHFAIPETLQDSAGFVPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKLD 325
                                    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       270       280       290       300       310       320     


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q60GU1_9RHIZ | Q60GU1 from UniProtKB/TrEMBL  Length:327

    Alignment length:324
                                    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       270       280       290       300       310       320    
         Q60GU1_9RHIZ     1 MQGKVALEEHFAIPETLQDSAGFVPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKL 324
               SCOP domains d2dvxb_ B: Thermophilic reversible gamma-resorcylate decarboxylase                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.eeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh....eeeee...............hhhhhhhhhhhhhhh..eeee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhh..............hhhhhhhhheeee.....hhhhhhhhhh..hhh.ee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dvx B   1 MQGKVALEEHFAIPETLQDSAGFVPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKL 324
                                    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       270       280       290       300       310       320    


Chain C from PDB  Type:PROTEIN  Length:323
 aligned with Q60GU1_9RHIZ | Q60GU1 from UniProtKB/TrEMBL  Length:327

    Alignment length:326
                                    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       270       280       290       300       310       320      
         Q60GU1_9RHIZ     1 MQGKVALEEHFAIPETLQDSAGFVPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKLDG 326
               SCOP domains d2dvxc_ C: Thermophi   lic reversible gamma-resorcylate decarboxylase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhhhhh..---..hhhhhhhhhhhhh..hhhhhhhhhh.eeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh..eeee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhh..............hhhhhhhhheeee.....hhhhhhhhhh..hhh.ee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dvx C   1 MQGKVALEEHFAIPETLQDS---VPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKLDG 326
                                    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       270       280       290       300       310       320      
                                              20  24                                                                                                                                                                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:321
 aligned with Q60GU1_9RHIZ | Q60GU1 from UniProtKB/TrEMBL  Length:327

    Alignment length:324
                                    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       270       280       290       300       310       320    
         Q60GU1_9RHIZ     1 MQGKVALEEHFAIPETLQDSAGFVPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKL 324
               SCOP domains d2dvxd_ D: Thermophi   lic reversible gamma-resorcylate decarboxylase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.hhhhhh..---..hhhhhhhhhhhhh..hhhhhhhhhh.eeeeeeee..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee...............hhhhhhhhhhhhhhh..eeee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhh..............hhhhhhhhheeee.....hhhhhhhhhhhhhhh.ee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dvx D   1 MQGKVALEEHFAIPETLQDS---VPGDYWKELQHRLLDIQDTRLKLMDAHGIETMILSLNAPAVQAIPDRRKAIEIARRANDVLAEECAKRPDRFLAFAALPLQDPDAATEELQRCVNDLGFVGALVNGFSQEGDGQTPLYYDLPQYRPFWGEVEKLDVPFYLHPRNPLPQDSRIYDGHPWLLGPTWAFAQETAVHALRLMASGLFDEHPRLNIILGHMGEGLPYMMWRIDHRNAWVKLPPRYPAKRRFMDYFNENFHITTSGNFRTQTLIDAILEIGADRILFSTDWPFENIDHASDWFNATSIAEADRVKIGRTNARRLFKL 324
                                    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       270       280       290       300       310       320    
                                              20  24
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DVX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q60GU1_9RHIZ | Q60GU1)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q60GU1_9RHIZ | Q60GU1: 2dvt 2dvu

(-) Related Entries Specified in the PDB File

2dvt 2dvu