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(-) Description

Title :  APO STRUCTURE OF SHORT-CHAIN ALCOHOL DEHYDROGENASE FROM RALSTONIA SP. DSM 6428
 
Authors :  H. Man, J. Kulig, D. Rother, G. Grogan
Date :  10 May 13  (Deposition) - 19 Mar 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Kred, Biocatalyst (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Man, K. Kedziora, J. Kulig, A. Frank, I. Lavandera, V. Gotor-Fernandez, D. Rother, S. Hart, J. P. Turkenburg, G. Grogan
Structures Of Alcohol Dehydrogenases From Ralstonia And Sphingobium Spp. Reveal The Molecular Basis For Their Recognition Of 'Bulky-Bulky' Ketones
Top. Catal. V. 57 356 2014
PubMed: search  |  Reference-DOI: 10.1007/S11244-013-0191-2

(-) Compounds

Molecule 1 - ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETYSBLIC-3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: RALSTONIA SP.
    Organism Taxid: 517192
    Strain: DSMZ 6428
    Synonym: ALCOHOL 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
1EDO8Ligand/Ion1,2-ETHANEDIOL
2TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:230 , ASP B:231 , SER B:233 , HOH B:2206 , HOH B:2209 , ARG C:25 , ARG C:216 , GLU C:218 , GLU C:219 , ALA C:222 , HOH C:2200BINDING SITE FOR RESIDUE TAM C1250
2AC2SOFTWAREGLY C:13 , ASN C:15 , GLY C:37 , ARG C:38 , ARG C:39 , HOH C:2024 , HOH C:2027BINDING SITE FOR RESIDUE EDO C1251
3AC3SOFTWARETHR A:166 , GLU A:167 , LYS A:169 , HOH A:2245 , GLN C:145BINDING SITE FOR RESIDUE EDO A1250
4AC4SOFTWAREASN D:6 , ASN D:53 , ARG D:78BINDING SITE FOR RESIDUE EDO D1250
5AC5SOFTWAREHOH B:2158 , THR D:166 , GLU D:167 , LEU D:168 , LYS D:169 , GLY D:170 , ARG D:171 , HOH D:2168 , HOH D:2169BINDING SITE FOR RESIDUE EDO D1251
6AC6SOFTWAREASP A:230 , ASP A:231 , SER A:233 , HOH A:2225 , HOH A:2226 , ARG D:216 , GLU D:218 , GLU D:219 , ALA D:222BINDING SITE FOR RESIDUE EDO D1252
7AC7SOFTWAREALA B:0 , MET B:1 , ARG B:3 , GLU B:29 , HOH B:2018 , HOH B:2229 , HOH B:2230 , PRO C:-1 , ALA C:0 , ARG C:3BINDING SITE FOR RESIDUE EDO B1250
8AC8SOFTWAREGLY B:13 , ASN B:15 , VAL B:36 , GLY B:37 , HOH B:2032 , HOH B:2036 , HOH B:2053 , HOH B:2080BINDING SITE FOR RESIDUE EDO B1251
9AC9SOFTWAREGLN C:93 , GLN C:145 , HIS C:147 , LEU C:201 , HOH C:2202BINDING SITE FOR RESIDUE EDO C1252

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BMN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BMN)

(-) 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:232
 aligned with C0IR58_9RALS | C0IR58 from UniProtKB/TrEMBL  Length:249

    Alignment length:252
                               1                                                                                                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  
         C0IR58_9RALS     - ---MYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAIDTPIIENQVSTQEEADELRAKFAAATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
               SCOP domains d4bmna_ A: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.......--------------------........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bmn A  -2 GPAMYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAIDTPI--------------------ATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187         -         -|      217       227       237       247  
                                                                                                                                                                                                                       187                  208                                         


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with C0IR58_9RALS | C0IR58 from UniProtKB/TrEMBL  Length:249

    Alignment length:253
                                1                                                                                                                                                                                                                                                        
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246   
         C0IR58_9RALS     - ----MYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAIDTPIIENQVSTQEEADELRAKFAAATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
               SCOP domains d4bmnb_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....----------------------.........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bmn B  -3 QGPAMYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAID----------------------AATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       | -         -         -|      216       226       236       246   
                                                                                                                                                                                                                     184                    207                                          


Chain C from PDB  Type:PROTEIN  Length:237
 aligned with C0IR58_9RALS | C0IR58 from UniProtKB/TrEMBL  Length:249

    Alignment length:252
                               1                                                                                                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  
         C0IR58_9RALS     - ---MYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAIDTPIIENQVSTQEEADELRAKFAAATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
               SCOP domains d4bmnc_ C: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....---------------hhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bmn C  -2 GPAMYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAID---------------ELRAKFAAATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      |  -         -  |    207       217       227       237       247  
                                                                                                                                                                                                                    184             200                                                 


Chain D from PDB  Type:PROTEIN  Length:229
 aligned with C0IR58_9RALS | C0IR58 from UniProtKB/TrEMBL  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
         C0IR58_9RALS     1 MYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAIDTPIIENQVSTQEEADELRAKFAAATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
               SCOP domains d4bmnd_ D: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....--------------------hhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bmn D   1 MYRLLNKTAVITGGNSGIGLATAKRFVAEGAYVFIVGRRRKELEQAAAEIGRNVTAVKADVTKLEDLDRLYAIVREQRGSIDVLFANSGAIEQKTLEEITPEHYDRTFDVNVRGLIFTVQKALPLLRDGGSVILTSSVAGVLGLQAHDTYSAAKAAVRSLARTWTTELKGRSIRVNAVSPGAID--------------------FAAATPLGRVGRPEELAAAVLFLASDDSSYVAGIELFVDGGLTQV 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   |     -         -    |  210       220       230       240         
                                                                                                                                                                                                                 184                  205
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (C0IR58_9RALS | C0IR58)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  4bmn
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 Related Entries

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

UniProtKB/TrEMBL
        C0IR58_9RALS | C0IR58: 4bms 4i5d 4i5e 4i5f 4i5g

(-) Related Entries Specified in the PDB File

4bms SHORT CHAIN ALCOHOL DEHYDROGENASE FROM RALSTONIA SP. DSM 6428 IN COMPLEX WITH NADPH
4bmv SHORT-CHAIN DEHYDROGENASE FROM SPHINGOBIUM YANOIKUYAE IN COMPLEX WITH NADPH