Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE D248A MUTANT OF 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS COMPLEXED WITH SUBSTRATE AT PH 8.5
 
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 :  1.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
10GY2Ligand/Ion(1E,3Z)-4-HYDROXYBUTA-1,3-DIENE-1,2,4-TRICARBOXYLICACID
20GZ2Ligand/Ion2-OXO-2H-PYRAN-4,6-DICARBOXYLIC ACID
3ACT2Ligand/IonACETATE ION
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
10GY1Ligand/Ion(1E,3Z)-4-HYDROXYBUTA-1,3-DIENE-1,2,4-TRICARBOXYLICACID
20GZ1Ligand/Ion2-OXO-2H-PYRAN-4,6-DICARBOXYLIC ACID
3ACT1Ligand/IonACETATE ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
10GY1Ligand/Ion(1E,3Z)-4-HYDROXYBUTA-1,3-DIENE-1,2,4-TRICARBOXYLICACID
20GZ1Ligand/Ion2-OXO-2H-PYRAN-4,6-DICARBOXYLIC ACID
3ACT1Ligand/IonACETATE ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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 , ASN A:253 , ACT A:402BINDING SITE FOR RESIDUE 0GZ A 401
2AC2SOFTWAREARG A:130 , ARG A:183 , ARG A:217 , ASN A:253 , 0GZ A:401 , 0GY A:403 , HOH A:651 , HOH A:705BINDING SITE FOR RESIDUE ACT A 402
3AC3SOFTWAREHIS 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:402BINDING SITE FOR RESIDUE 0GY A 403
4AC4SOFTWAREHIS B:31 , HIS B:33 , TYR B:49 , SER B:77 , ARG B:124 , ARG B:130 , LEU B:131 , TYR B:156 , HIS B:180 , ARG B:183 , ARG B:217 , PRO B:252 , ASN B:253 , ACT B:402 , HOH B:698BINDING SITE FOR RESIDUE 0GZ B 401
5AC5SOFTWAREARG B:130 , ARG B:183 , ARG B:217 , ASN B:253 , 0GY B:405 , HOH B:735 , HOH B:826BINDING SITE FOR RESIDUE ACT B 402
6AC6SOFTWAREHOH B:591 , HOH B:688 , HOH B:701 , HOH B:741 , HOH B:759 , HOH B:783BINDING SITE FOR RESIDUE MG B 403
7AC7SOFTWAREHOH B:630 , HOH B:674 , HOH B:719 , HOH B:737 , HOH B:781BINDING SITE FOR RESIDUE MG B 404
8AC8SOFTWAREHIS B:31 , HIS B:33 , TYR B:49 , ALA B:76 , SER B:77 , ARG B:124 , ARG B:130 , LEU B:131 , TYR B:156 , HIS B:180 , ARG B:183 , ARG B:217 , PRO B:252 , ASN B:253 , ACT B:402 , HOH B:698BINDING SITE FOR RESIDUE 0GY B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DI8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:36 -Pro A:37
2Pro A:223 -Pro A:224
3Trp A:249 -Pro A:250
4Gly B:36 -Pro B:37
5Pro B:223 -Pro B:224
6Trp B:249 -Pro B:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DI8)

(-) Exons   (0, 0)

(no "Exon" information available for 4DI8)

(-) 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:294
 aligned with PDCH_SPHPI | O87170 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:294
                             1                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289    
           PDCH_SPHPI     - -MTNDERILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLGFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNFLKRLVDDAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWGTDWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 293
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........................eeeee......................hhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhh...eeeee......hhhhhhhhhhh.eeeeeee.........hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eee.hhhh.hhhhh..hhhhhhhhhhhh....eeee..hhhhhh.....hhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4di8 A   2 SLTNDERILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLGFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNFLKRLVDDAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWGTAWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291    


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with PDCH_SPHPI | O87170 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:294
                             1                                                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289    
           PDCH_SPHPI     - -MTNDERILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLGFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNFLKRLVDDAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWGTDWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 293
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........................eeeee......................hhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhh...eeeee......hhhhhhhhhhh.eeeeeee.........hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eee.hhhh.hhhhh..hhhhhhhhhhhh....eeee..hhhhhh.....hhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4di8 B   2 SLTNDERILSWNETPSKPRYTPPPGAIDAHCHVFGPMAQFPFSPKAKYLPRDAGPDMLFALRDHLGFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFNFLKRLVDDAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMGRPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADYADRVIWGTAWPHPNMQDAIPDDGLVVDMIPRIAPTPELQHKMLVTNPMRLYWSEEM 295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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  (0, 0)

(no "SCOP Domain" information available for 4DI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DI8)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    0GY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    0GZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:36 - Pro A:37   [ RasMol ]  
    Gly B:36 - Pro B:37   [ RasMol ]  
    Pro A:223 - Pro A:224   [ RasMol ]  
    Pro B:223 - Pro B:224   [ RasMol ]  
    Trp A:249 - Pro A:250   [ RasMol ]  
    Trp B:249 - Pro B:250   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4di8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PDCH_SPHPI | O87170
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PDCH_SPHPI | O87170
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDCH_SPHPI | O87170: 4d8l 4di9 4dia

(-) Related Entries Specified in the PDB File

2qah 4d8l 4di9 4dia