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(-) Description

Title :  CRYSTAL STRUCTURE OF SCYLLO-INOSITOL DEHYDROGENASE FROM LACTOBACILLUS CASEI WITH BOUND COFACTOR NAD(H) AND SCYLLO-INOSITOL
 
Authors :  D. Bertwistle, D. A. R. Sanders, D. R. J. Palmer
Date :  09 Oct 13  (Deposition) - 15 Apr 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrogen Bonding, Nad, Sugar Alcohol Dehydrogenases, Rossmann Fold, Dehydrogenate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Bertwistle, H. Aamudalapalli, D. A. R. Sanders, D. R. J. Palmer
Crystal Structure Of Scyllo-Inositol Dehydrogenase From Lactobacillus Casei With Bound Cofactor Nad(H) And Scyllo-Inositol
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INOSITOL DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-80L
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 4-343
    Gene: IDH, IOLG, IOLG2, LCABL_02220
    Organism Scientific: LACTOBACILLUS CASEI
    Organism Taxid: 543734
    Strain: BL23
    Synonym: SCYLLO-INOSITOL DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
12H33Ligand/Ion(1R,2R,3R,4R,5R,6R)-CYCLOHEXANE-1,2,3,4,5,6-HEXOL
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:11 , GLY A:12 , LEU A:13 , GLY A:14 , ARG A:15 , LEU A:16 , SER A:38 , VAL A:39 , VAL A:40 , GLU A:43 , VAL A:75 , SER A:76 , PRO A:77 , SER A:78 , PHE A:80 , HIS A:81 , GLU A:98 , LYS A:99 , MET A:128 , PHE A:170 , ASP A:182 , HIS A:186 , PHE A:287 , PHE A:295 , 2H3 A:402 , HOH A:547BINDING SITE FOR RESIDUE NAI A 401
2AC2SOFTWAREARG A:15 , LYS A:99 , ASP A:159 , ASP A:182 , MET A:183 , HIS A:186 , ARG A:241 , TYR A:247 , PHE A:287 , NAI A:401 , HOH A:501BINDING SITE FOR RESIDUE 2H3 A 402
3AC3SOFTWAREVAL B:11 , LEU B:13 , GLY B:14 , ARG B:15 , LEU B:16 , SER B:38 , VAL B:39 , VAL B:40 , GLU B:43 , VAL B:75 , SER B:76 , PRO B:77 , SER B:78 , PHE B:80 , HIS B:81 , GLU B:98 , LYS B:99 , MET B:128 , PHE B:170 , ASP B:182 , HIS B:186 , PHE B:287 , 2H3 B:402BINDING SITE FOR RESIDUE NAI B 401
4AC4SOFTWAREARG B:15 , LYS B:99 , ASP B:159 , ASP B:182 , MET B:183 , HIS B:186 , ARG B:241 , TYR B:247 , PHE B:287 , NAI B:401 , HOH B:521BINDING SITE FOR RESIDUE 2H3 B 402
5AC5SOFTWAREGLY C:12 , LEU C:13 , GLY C:14 , ARG C:15 , LEU C:16 , SER C:38 , VAL C:39 , GLU C:43 , VAL C:75 , SER C:76 , PRO C:77 , SER C:78 , PHE C:80 , HIS C:81 , GLU C:98 , LYS C:99 , MET C:128 , HIS C:186BINDING SITE FOR RESIDUE NAI C 400
6AC6SOFTWARELEU D:13 , GLY D:14 , ARG D:15 , LEU D:16 , SER D:38 , VAL D:39 , GLU D:43 , SER D:76 , PRO D:77 , PHE D:80 , HIS D:81 , GLU D:98 , LYS D:99 , GLY D:126 , MET D:128 , PHE D:170 , HIS D:186 , PHE D:287 , 2H3 D:402BINDING SITE FOR RESIDUE NAI D 401
7AC7SOFTWARELYS D:99 , ASP D:159 , ASP D:182 , MET D:183 , HIS D:186 , TYR D:247 , NAI D:401BINDING SITE FOR RESIDUE 2H3 D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N54)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Lys A:99 -Pro A:100
2Lys B:99 -Pro B:100
3Lys C:99 -Pro C:100
4Ser C:176 -Gly C:177
5Lys D:99 -Pro D:100
6Ser D:176 -Gly D:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N54)

(-) Exons   (0, 0)

(no "Exon" information available for 4N54)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh..eee.hhhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhhh....eeeeeeee....eeeeeeeeee....eeeeeeee...eeee........eeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n54 A   4 KTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDMSIHDIDVIRWFTGKEIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVNSILNNQDVGITAEDGLQGTKAALALQEAFEKNDIVQVAS 343
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh..eee.hhhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhhh....eeeeeeee....eeeeeeeeee....eeeeeeee...eeee........eeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n54 B   4 KTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDMSIHDIDVIRWFTGKEIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVNSILNNQDVGITAEDGLQGTKAALALQEAFEKNDIVQVAS 343
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343


Chain C from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh..eee.hhhhhhhhh...eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhh.....eeeeeeee....eeeeeeeeee....eeeeeeee...eeee........eeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n54 C   4 KTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDMSIHDIDVIRWFTGKEIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVNSILNNQDVGITAEDGLQGTKAALALQEAFEKNDIVQVAS 343
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343


Chain D from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh...eeeeeee.....hhhhhhhh........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhh...eeeeeeee....eeeeeeeeee....eeeeeeee...eeee........eeeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n54 D   4 KTIKIGIVGLGRLGKIHATNIATKIQHAKLQAATSVVPAELDWAKKELGVEEVFEDFDDMVQHADIDAVFIVSPSGFHLQQIESALNAGKHVFSEKPIGLDIEAIEHTQQVIAQHANLKFQLGFMRRFDDSYRYAKQLVDQGKIGDITLIRSYSIDPAAGMASFVKFATSANSGGLFLDMSIHDIDVIRWFTGKEIDKVWAIGLNRAYPVLDKAGELETGAALMQLEDKTMAILVAGRNAAHGYHVETEIIGTKGMLRIAQVPEKNLVTVMNEEGIIRPTSQNFPERFAQAFLSEEQAFVNSILNNQDVGITAEDGLQGTKAALALQEAFEKNDIVQVAS 343
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
   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 4N54)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N54)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N54)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4N54)

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  Cis Peptide Bonds
    Lys A:99 - Pro A:100   [ RasMol ]  
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    Lys D:99 - Pro D:100   [ RasMol ]  
    Ser C:176 - Gly C:177   [ RasMol ]  
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 Related Entries

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(-) Related Entries Specified in the PDB File

3cea 4mie 4mio 4miy 4mkx 4mkz