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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D248A MUTANT OF 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS COMPLEXED WITH SUBSTRATE AT PH 6.5
 
Authors :  V. N. Malashkevich, R. Toro, M. E. Hobbs, F. M. Raushel, S. C. Almo
Date :  11 Jan 12  (Deposition) - 03 Oct 12  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Hobbs, V. Malashkevich, H. J. Williams, C. Xu, J. M. Sauder, S. K. Burley, S. C. Almo, F. M. Raushel
Structure And Catalytic Mechanism Of Ligi: Insight Into The Amidohydrolase Enzymes Of Cog3618 And Lignin Degradation.
Biochemistry V. 51 3497 2012
PubMed-ID: 22475079  |  Reference-DOI: 10.1021/BI300307B

(-) Compounds

Molecule 1 - 2-PYRONE-4,6-DICARBAXYLATE HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LIGI
    Mutation: YES
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Strain: SYK-6
    Synonym: 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
10GY1Ligand/Ion(1E,3Z)-4-HYDROXYBUTA-1,3-DIENE-1,2,4-TRICARBOXYLICACID
2ACT1Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:31 , HIS A:33 , TYR A:49 , ALA A:76 , SER A:77 , ARG A:124 , ARG A:130 , LEU A:131 , TYR A:156 , HIS A:180 , ARG A:183 , ARG A:217 , PRO A:252 , ASN A:253 , ACT A:402 , HOH A:653BINDING SITE FOR RESIDUE 0GY A 401
2AC2SOFTWAREARG A:130 , ARG A:183 , ARG A:217 , ASN A:253 , 0GY A:401 , HOH A:573 , HOH A:744BINDING SITE FOR RESIDUE ACT A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DI9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:36 -Pro A:37
2Pro A:223 -Pro A:224
3Trp A:249 -Pro A:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DI9)

(-) Exons   (0, 0)

(no "Exon" information available for 4DI9)

(-) 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:293
 aligned with PDCH_SPHPI | O87170 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:293
                                    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   
           PDCH_SPHPI     1 MTNDERILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLGFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNFLKRLVDDAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWGTDWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...................eeeee......................hhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhh...eeeee......hhhhhhhhhhh.eeeeeee.........hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eee.hhhh.hhhhh..hhhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di9 A   3 LTNDERILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLGFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNFLKRLVDDAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWGTAWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 295
                                    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       292
   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 4DI9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DI9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDCH_SPHPI | O87170)
molecular function
    GO:0047554    2-pyrone-4,6-dicarboxylate lactonase activity    Catalysis of the reaction: 2-oxo-2H-pyran-4,6-dicarboxylate + H(2)O = 4-carboxy-2-hydroxyhexa-2,4-dienedioate + H(+).
    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.
biological process
    GO:0019619    3,4-dihydroxybenzoate catabolic process    The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDCH_SPHPI | O87170: 4d8l 4di8 4dia

(-) Related Entries Specified in the PDB File

2qah 4d8l 4di8 4dia