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

(-) Description

Title :  5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
 
Authors :  H. S. Subramanya, D. I. Roper, Z. Dauter, E. J. Dodson, G. J. Davies, K. S. D. B. Wigley
Date :  09 Nov 95  (Deposition) - 03 Apr 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydroxymuconate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Subramanya, D. I. Roper, Z. Dauter, E. J. Dodson, G. J. Davies, K. S. Wilson, D. B. Wigley
Enzymatic Ketonization Of 2-Hydroxymuconate: Specificity An Mechanism Investigated By The Crystal Structures Of Two Isomerases.
Biochemistry V. 35 792 1996
PubMed-ID: 8547259  |  Reference-DOI: 10.1021/BI951732K

(-) Compounds

Molecule 1 - 5-CARBOXYMETHYL-2-HYDROXYMUCONATE ISOMERASE
    Chains: A, B, C
    EC Number: 5.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: CHM
    Expression System Plasmid: PUC19
    Expression System Taxid: 562
    Gene: CHM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 498388
    Other Details: CHMI PROMOTER
    Strain: C

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:2 , PRO A:36 , GLY A:69 , ARG A:72BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREPRO B:2 , PRO B:36 , ILE B:68 , GLY B:69 , ARG B:72BINDING SITE FOR RESIDUE SO4 B 127
3AC3SOFTWAREPRO C:2 , ILE C:68 , GLY C:69 , ARG C:72 , HOH C:182BINDING SITE FOR RESIDUE SO4 C 127
4AC4SOFTWAREGLY A:39 , ARG A:41 , LYS A:117 , ASN A:119 , HIS A:122 , HOH B:172BINDING SITE FOR RESIDUE SO4 A 128
5AC5SOFTWAREGLY B:39 , ARG B:41 , LYS B:117 , ASN B:119 , HIS B:122 , HOH B:136 , HOH B:169 , HOH B:173BINDING SITE FOR RESIDUE SO4 B 128
6AC6SOFTWAREGLY C:39 , ARG C:41 , LYS C:117 , ASN C:119 , HIS C:122 , HOH C:178BINDING SITE FOR RESIDUE SO4 C 128

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OTG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OTG)

(-) 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:125
 aligned with HPCD_ECOLX | Q05354 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
           HPCD_ECOLX     2 PHFIVECSDNIREEADLPGLFAKVNPTLAATGIFPLAGIRSRVHWVDTWQMADGQHDYASVHMTLKIGAGRSLESRQQAGEMLFELIKTHFAALMESRLLALSFEIEELHPTLNFKQNNVHALFK 126
               SCOP domains d1otga_ A: 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI)                                                                 SCOP domains
               CATH domains 1otgA00 A:2-126 Macrophage Migration Inhibitory Factor                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhhhhhh.hhhhhhhhhhhhh......hhh.eeeeeee..eee......eeeeeeeeee.....hhhhhhhhhhhhhhhhhh.hhhh...eeeeeeeeee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otg A   2 PHFIVECSDNIREEADLPGLFAKVNPTLAATGIFPLAGIRSRVHWVDTWQMADGQHDYAFVHMTLKIGAGRSLESRQQAGEMLFELIKTHFAALMESRLLALSFEIEELHPTLNFKQNNVHALFK 126
                                    11        21        31        41        51        61        71        81        91       101       111       121     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with HPCD_ECOLX | Q05354 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
           HPCD_ECOLX     2 PHFIVECSDNIREEADLPGLFAKVNPTLAATGIFPLAGIRSRVHWVDTWQMADGQHDYASVHMTLKIGAGRSLESRQQAGEMLFELIKTHFAALMESRLLALSFEIEELHPTLNFKQNNVHALFK 126
               SCOP domains d1otgb_ B: 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI)                                                                 SCOP domains
               CATH domains 1otgB00 B:2-126 Macrophage Migration Inhibitory Factor                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhh.....hhhhhhhhhhhhhhh....hhh.eeeeeee.eeee.......eeeeeeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh..eeeeeeeee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otg B   2 PHFIVECSDNIREEADLPGLFAKVNPTLAATGIFPLAGIRSRVHWVDTWQMADGQHDYAFVHMTLKIGAGRSLESRQQAGEMLFELIKTHFAALMESRLLALSFEIEELHPTLNFKQNNVHALFK 126
                                    11        21        31        41        51        61        71        81        91       101       111       121     


Chain C from PDB  Type:PROTEIN  Length:125
 aligned with HPCD_ECOLX | Q05354 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
           HPCD_ECOLX     2 PHFIVECSDNIREEADLPGLFAKVNPTLAATGIFPLAGIRSRVHWVDTWQMADGQHDYASVHMTLKIGAGRSLESRQQAGEMLFELIKTHFAALMESRLLALSFEIEELHPTLNFKQNNVHALFK 126
               SCOP domains d1otgc_ C: 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI)                                                                 SCOP domains
               CATH domains 1otgC00 C:2-126 Macrophage Migration Inhibitory Factor                                                                        CATH domains
           Pfam domains (1) CHMI-1otgC01 C:2-125                                                                                                        - Pfam domains (1)
           Pfam domains (2) CHMI-1otgC02 C:2-125                                                                                                        - Pfam domains (2)
           Pfam domains (3) CHMI-1otgC03 C:2-125                                                                                                        - Pfam domains (3)
         Sec.struct. author .eeeeeeehhh.....hhhhhhhhhhhhhhh....hhh.eeeeeee..eee......eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.....eeeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otg C   2 PHFIVECSDNIREEADLPGLFAKVNPTLAATGIFPLAGIRSRVHWVDTWQMADGQHDYAFVHMTLKIGAGRSLESRQQAGEMLFELIKTHFAALMESRLLALSFEIEELHPTLNFKQNNVHALFK 126
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: MIF (36)
(-)
Family: CHMI (1)
(-)
Escherichia coli (1)
1aCHMI-1otgC01C:2-125
1bCHMI-1otgC02C:2-125
1cCHMI-1otgC03C:2-125

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (HPCD_ECOLX | Q05354)
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: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:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1otg)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1otg
    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
  HPCD_ECOLX | Q05354
    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)
  5.3.2.-
    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
  HPCD_ECOLX | Q05354
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1OTG)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1OTG)