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(-) Description

Title :  CRYSTAL STRUCTURE OF A12K/D35S MUTANT MYO-INOSITOL DEHYDROGENASE FROM BACILLUS SUBTILIS WITH BOUND COFACTOR NADP
 
Authors :  D. Bertwistle, D. A. R. Sanders, D. R. J. Palmer
Date :  18 Jun 13  (Deposition) - 04 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cofactor, Binding Sites, Catalysis, Hydrogen Bonding, Inositol, Kinetics, Sugar Alcohol Dehydrogenase, Rossmann Fold, Nadp Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zheng, D. Bertwistle, D. A. Sanders, D. R. Palmer
Converting Nad-Specific Inositol Dehydrogenase To An Efficient Nadp-Selective Catalyst, With A Surprising Twist.
Biochemistry V. 52 5876 2013
PubMed-ID: 23952058  |  Reference-DOI: 10.1021/BI400821S

(-) Compounds

Molecule 1 - INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3-DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-337
    Gene: BSU39700, E83G, IDH, IOLG
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: MYO-INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3- DEHYDROGENASE, MI 2-DEHYDROGENASE/DCI 3-DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:12 , ILE A:13 , THR A:73 , SER A:74 , TRP A:75 , GLY A:76 , HIS A:79 , GLU A:96 , LYS A:97 , PRO A:98 , GLY A:124 , MET A:126 , HIS A:176 , TRP A:272 , TYR A:280 , HOH A:535BINDING SITE FOR RESIDUE NAP A 401
2AC2SOFTWAREASP A:130 , SER A:131 , GLY A:132 , PRO A:251 , ARG A:275BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWARETYR A:129 , ASP A:130 , SER A:131 , ALA A:278 , ALA A:279 , HOH A:532BINDING SITE FOR RESIDUE EDO A 403
4AC4SOFTWAREGLY B:11 , LYS B:12 , ILE B:13 , THR B:73 , SER B:74 , TRP B:75 , GLY B:76 , HIS B:79 , GLU B:96 , LYS B:97 , GLY B:124 , MET B:126 , TRP B:272 , TYR B:280 , HOH B:508BINDING SITE FOR RESIDUE NAP B 400
5AC5SOFTWARELYS B:330 , GLU B:331 , GLY C:11 , LYS C:12 , ILE C:13 , TRP C:75 , HIS C:79 , GLU C:96 , LYS C:97 , PRO C:98 , GLY C:124 , MET C:126 , TRP C:272 , TYR C:280BINDING SITE FOR RESIDUE NAP C 401
6AC6SOFTWARESER C:191 , GLN C:193 , VAL C:214 , GLU C:216BINDING SITE FOR RESIDUE EDO C 402
7AC7SOFTWAREASP C:130 , GLY C:132 , ARG C:275BINDING SITE FOR RESIDUE EDO C 403
8AC8SOFTWARETHR D:10 , GLY D:11 , LYS D:12 , ILE D:13 , SER D:35 , ASN D:37 , THR D:73 , SER D:74 , TRP D:75 , HIS D:79 , GLU D:96 , LYS D:97 , PRO D:98 , GLY D:124 , MET D:126 , HIS D:176 , TRP D:272 , TYR D:280BINDING SITE FOR RESIDUE NAP D 401
9AC9SOFTWAREASP D:130 , SER D:131 , GLY D:132 , ARG D:275BINDING SITE FOR RESIDUE EDO D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L8V)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological 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
5Ser C:35 -Val C:36
6Val C:36 -Asn C:37
7Lys C:97 -Pro C:98
8Asp C:209 -Pro C:210
9Lys D:97 -Pro D:98
10Asp D:209 -Pro D:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L8V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L8V)

(-) Exons   (0, 0)

(no "Exon" information available for 4L8V)

(-) 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: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..eeee.......eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l8v A   1 MSLRIGVIGTGKIGKEHINRITNKLSGAEIVAVTSVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 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
                                                                                                                                                                                                                                                                                                                                                                                 
               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.......eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l8v B   1 MSLRIGVIGTGKIGKEHINRITNKLSGAEIVAVTSVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 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 C from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh...ee..hhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeee..........hhhhhh.hhhhhhhhhhhhh..eeeeeee...............eeeeeee....eeeeeee.......eeeeeeee...eee.......eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l8v C   1 MSLRIGVIGTGKIGKEHINRITNKLSGAEIVAVTSVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 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 D from PDB  Type:PROTEIN  Length: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.......eeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l8v D   1 MSLRIGVIGTGKIGKEHINRITNKLSGAEIVAVTSVNQEAAQKVVEQYQLNATVYPNDDSLLADENVDAVLVTSWGPAHESSVLKAIKAQKYVFCEKPLATTAEGCMRIVEEEIKVGKRLVQVGFMRRYDSGYVQLKEALDNHVIGEPLMIHCAHRNPTVGDNYTTDMAVVDTLVHEIDVLHWLVNDDYESVQVIYPKKSKNALPHLKDPQIVVIETKGGIVINAEIYVNCKYGYDIQCEIVGEDGIIKLPEPSSISLRKEGRFSTDILMDWQRRFVAAYDVEIQDFIDSIQKKGEVSGPTAWDGYIAAVTTDACVKAQESGQKEKVELKEKPEFYQ 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)
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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 4L8V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L8V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L8V)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  4l8v
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  1.1.1.18
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 Related Entries

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        IOLG_BACSU | P26935: 3mz0 3nt2 3nt4 3nt5 3nto 3ntq 3ntr 4l9r

(-) Related Entries Specified in the PDB File

3mz0 3nt2 3nt4 3nt5 3nto 3ntq 4l9r