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(-) Description

Title :  CRYSTAL STRUCTURE OF MYO-INOSITOL DEHYDROGENASE FROM BACILLUS SUBTILIS WITH BOUND COFACTOR
 
Authors :  K. E. Van Straaten, D. R. J. Palmer, D. A. R. Sanders
Date :  02 Jul 10  (Deposition) - 15 Sep 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Bsidh, Oxidoreductase, N-Terminal Rossmann Fold Domain, Glyceraldehyde-3-Phosphate Like C-Terminal Domain, Nad, Myo-Inositol (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, B
    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
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1NAD3Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2NAI3Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:9 , GLY A:11 , ALA A:12 , ILE A:13 , ASP A:35 , VAL A:36 , ASN A:37 , GLN A:42 , THR A:73 , SER A:74 , TRP A:75 , GLY A:76 , ALA A:78 , HIS A:79 , GLU A:96 , LYS A:97 , GLY A:124 , HIS A:176 , TYR A:280 , HOH A:367 , HOH A:407BINDING SITE FOR RESIDUE NAD A 400
2AC2SOFTWAREGLY B:9 , GLY B:11 , ALA B:12 , ILE B:13 , ASP B:35 , VAL B:36 , SER B:74 , TRP B:75 , ALA B:78 , HIS B:79 , LYS B:97 , PRO B:98 , HIS B:176 , TRP B:272 , TYR B:280BINDING SITE FOR RESIDUE NAI B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NT2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:97 -Pro A:98
2Asp A:209 -Pro A:210
3Lys B:97 -Pro B:98
4Asp B:209 -Pro B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NT2)

(-) Exons   (0, 0)

(no "Exon" information available for 3NT2)

(-) 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:337
 aligned with IOLG_BACSU | P26935 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:337
                                    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 MSLRIGVIGTGAIGKEHINRITNKLSGAEIVAVTDVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee...............eeeeeee....eeeeeee.......eeeeeeee...eee........eee..eee.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eee......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nt2 A   1 MSLRIGVIGTGAIGKEHINRITNKLSGAEIVAVTDVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 337
                                    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       


Chain B from PDB  Type:PROTEIN  Length:337
 aligned with IOLG_BACSU | P26935 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:337
                                    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 MSLRIGVIGTGAIGKEHINRITNKLSGAEIVAVTDVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --GFO_IDH_MocA-3nt2B01 B:3-125                                                                                               -----------GFO_IDH_MocA_C-3nt2B03 B:137-240                                                                        ------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --GFO_IDH_MocA-3nt2B02 B:3-125                                                                                               -----------GFO_IDH_MocA_C-3nt2B04 B:137-240                                                                        ------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh....eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee...............eeeeeee....eeeeeee.......eeeeeeee...eee........eee..eee.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nt2 B   1 MSLRIGVIGTGAIGKEHINRITNKLSGAEIVAVTDVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 337
                                    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 3NT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NT2)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (5, 5)

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

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 Related Entries

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

UniProtKB/Swiss-Prot
        IOLG_BACSU | P26935: 3mz0 3nt4 3nt5 3nto 3ntq 3ntr 4l8v 4l9r

(-) Related Entries Specified in the PDB File

3mz0 APO-IDH
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