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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF K97V MUTANT MYO-INOSITOL DEHYDROGENASE FROM BACILLUS SUBTILIS
 
Authors :  K. E. Van Straaten, D. R. J. Palmer, D. A. R. Sanders
Date :  05 Jul 10  (Deposition) - 15 Sep 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  K97V Mutant, Bsidh, Oxidoreductase, N-Terminal Rossmann Fold Domain, Glyceraldehyde-3-Phosphate Like C-Terminal Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Van Straaten, H. Zheng, D. R. Palmer, D. A. Sanders
Structural Investigation Of Myo-Inositol Dehydrogenase From Bacillus Subtilis: Implications For Catalytic Mechanism And Inositol Dehydrogenase Subfamily Classification.
Biochem. J. V. 432 237 2010
PubMed-ID: 20809899  |  Reference-DOI: 10.1042/BJ20101079

(-) Compounds

Molecule 1 - INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3-DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHISTEV
    Expression System Strain: ROSETTA
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: BSU39700, E83G, IDH, IOLG, NP_391849.2
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: MYO-INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3- DEHYDROGENASE, MI 2-DEHYDROGENASE/DCI 3-DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EPE4Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:160 , GLY A:161 , TYR A:164 , ASP A:172 , THR A:173 , TYR A:235 , TRP A:272 , HOH A:683BINDING SITE FOR RESIDUE EPE A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NTO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:97 -Pro A:98
2Asp A:209 -Pro A:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NTO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NTO)

(-) Exons   (0, 0)

(no "Exon" information available for 3NTO)

(-) 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:338
 aligned with IOLG_BACSU | P26935 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:338
                                    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       330        
           IOLG_BACSU     1 MSLRIGVIGTGAIGKEHINRITNKLSGAEIVAVTDVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQS 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --GFO_IDH_MocA-3ntoA01 A:3-125                                                                                               -----------GFO_IDH_MocA_C-3ntoA02 A:137-240                                                                        -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....ee..hhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee...............eeeeeee....eeeeeee.......eeeeeeee...eee.......eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nto A   1 MSLRIGVIGTGAIGKEHINRITNKLSGAEIVAVTDVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEVPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQS 338
                                    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       330
   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 3NTO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NTO)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: ox_reductase_C (19)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (IOLG_BACSU | P26935)
molecular function
    GO:0050112    inositol 2-dehydrogenase activity    Catalysis of the reaction: myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + H(+) + NADH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0019310    inositol catabolic process    The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
    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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 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
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:209 - Pro A:210   [ RasMol ]  
    Val A:97 - Pro A:98   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  3nto
    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
  IOLG_BACSU | P26935
    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)
  1.1.1.18
    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
  IOLG_BACSU | P26935
    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
        IOLG_BACSU | P26935: 3mz0 3nt2 3nt4 3nt5 3ntq 3ntr 4l8v 4l9r

(-) Related Entries Specified in the PDB File

3mz0 APO-IDH
3nt2 IDH WITH BOUND COFACTOR
3nt4 IDH WITH BOUND COFACTOR AND INOSITOL
3nt5 IDH WITH BOUND COFACTOR AND INOSOSE
3ntq K97V MUTANT IDH WITH BOUND COFACTOR
3ntr K97V MUTANT IDH WITH BOUND COFACTOR AND INOSITOL