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(-) Description

Title :  T190S MUTANT OF D-3-HYDROXYBUTYRATE DEHYDROGENASE
 
Authors :  K. Nakashima, Y. Nakajima, K. Ito, T. Yoshimoto
Date :  07 Oct 08  (Deposition) - 25 Aug 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Short Chain Dehydrogenase Redactase, Sdr Family, Nad, Nadh, Hbdh, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nakashima, K. Ito, Y. Nakajima, R. Yamazawa, S. Miyakawa, T. Yoshimoto
Closed Complex Of The D-3-Hydroxybutyrate Dehydrogenase Induced By An Enantiomeric Competitive Inhibitor.
J. Biochem. V. 145 467 2009
PubMed-ID: 19122202  |  Reference-DOI: 10.1093/JB/MVN186
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D(-)-3-HYDROXYBUTYRATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK233-3
    Expression System Strain: XL1BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS FRAGI
    Organism Taxid: 296

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
13HL1Ligand/Ion(3S)-3-HYDROXYBUTANOIC ACID
2MG2Ligand/IonMAGNESIUM ION
3NAD3Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , ASN A:34 , GLY A:35 , PHE A:36 , ALA A:62 , ASP A:63 , LEU A:64 , ASN A:90 , GLY A:92 , LEU A:113 , ILE A:140 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , VAL A:188 , SER A:190 , PRO A:191 , LEU A:192 , VAL A:193 , 3HL A:301 , HOH A:1087 , HOH A:1097 , HOH A:1229 , HOH A:1255BINDING SITE FOR RESIDUE NAD A 300
2AC2SOFTWAREGLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , LEU A:192 , GLN A:196 , NAD A:300BINDING SITE FOR RESIDUE 3HL A 301
3AC3SOFTWAREARG A:260 , HOH A:1167 , ARG D:260 , HOH D:1018 , HOH D:1318BINDING SITE FOR RESIDUE MG A 406
4AC4SOFTWAREARG B:260 , HOH B:1013 , HOH B:1135 , ARG C:260 , HOH C:1102 , HOH C:1367BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWAREGLY C:11 , THR C:13 , SER C:14 , GLY C:15 , ILE C:16 , ASN C:34 , GLY C:35 , PHE C:36 , ALA C:62 , ASP C:63 , LEU C:64 , ASN C:90 , GLY C:92 , LEU C:113 , ILE C:140 , ALA C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , TRP C:187 , VAL C:188 , SER C:190 , PRO C:191 , LEU C:192 , VAL C:193 , HOH C:1011BINDING SITE FOR RESIDUE NAD C 300
6AC6SOFTWAREGLY D:11 , THR D:13 , SER D:14 , GLY D:15 , ILE D:16 , ASN D:34 , GLY D:35 , PHE D:36 , ALA D:62 , ASP D:63 , LEU D:64 , ASN D:90 , ALA D:91 , GLY D:92 , LEU D:113 , ILE D:140 , ALA D:141 , SER D:142 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , TRP D:187 , VAL D:188 , SER D:190 , LEU D:192 , VAL D:193 , HOH D:1083 , HOH D:1176BINDING SITE FOR RESIDUE NAD D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZTM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZTM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZTM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZTM)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZTM)

(-) 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:255
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:255
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
         Q5KST5_PSEFR     6 VAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d2ztma_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2ztmA00 A:6-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhh.........eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztm A   6 VAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRSPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:256
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
         Q5KST5_PSEFR     5 KVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d2ztmb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2ztmB00 B:5-260 NAD(P)-binding R           ossmann-like Domain                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh..eeeee..-----------hhhhhh....eee.....hhhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....---------------------hhhhhhhhh......hhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztm B   5 KVAVVTGSTSGIGLGIATALAAQGADIVLNGF-----------GLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRS---------------------ARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    14        24        34 |       -   |    54        64        74        84        94       104       114       124       134       144       154       164       174       184     |   -         -       214       224       234       244       254      
                                                          36          48                                                                                                                                           190                   212                                                


Chain C from PDB  Type:PROTEIN  Length:250
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         Q5KST5_PSEFR     1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d2ztmc_ C: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztmC00 C:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhh.----------.hhhhhh......hhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztm C   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRSPLVEKQISALAEK----------ELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  |      -   |   220       230       240       250       260
                                                                                                                                                                                                                                    203        214                                              


Chain D from PDB  Type:PROTEIN  Length:247
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         Q5KST5_PSEFR     1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d2ztmd_ D: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztmD00 D:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----adh_short-2ztmD01 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----adh_short-2ztmD02 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----adh_short-2ztmD03 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----adh_short-2ztmD04 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh.-------------..hhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztm D   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRSPLVEKQISA-------------RELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        |-         -  |    220       230       240       250       260
                                                                                                                                                                                                                                199           213
   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  (1, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5KST5_PSEFR | Q5KST5)
molecular function
    GO:0003858    3-hydroxybutyrate dehydrogenase activity    Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + H(+) + NADH.
    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.
    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: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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  2ztm
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 Related Entries

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

UniProtKB/TrEMBL
        Q5KST5_PSEFR | Q5KST5: 1wmb 1x1t 2ztl 2ztu 2ztv

(-) Related Entries Specified in the PDB File

1wmb THE WILD-TYPE ENZYME WITH OPEN CONFORMATION
1x1t THE WILD-TYPE ENZYME COMPLEXED WITH NAD+
2ztl TERNARY COMPLEX OF THE WILD-TYPE ENZYME WITH CLOSED CONFORMATION