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(-) Description

Title :  T190A MUTANT OF D-3-HYDROXYBUTYRATE DEHYDROGENASE COMPLEXED WITH NAD+
 
Authors :  K. Nakashima, Y. Nakajima, K. Ito, T. Yoshimoto
Date :  09 Oct 08  (Deposition) - 25 Aug 09  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Short Chain Dehydrogenase/Reductase, 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  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NAD3Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
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 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , TRP A:187 , VAL A:188 , HOH A:1160 , HOH A:1544BINDING SITE FOR RESIDUE NAD A 300
2AC2SOFTWAREARG A:260 , HOH A:1003 , ARG D:260 , HOH D:1004 , HOH D:1005 , HOH D:1006BINDING SITE FOR RESIDUE MG A 406
3AC3SOFTWAREVAL B:147 , ARG B:260 , HOH B:1001 , ARG C:260 , HOH C:1002BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWAREGLY C:11 , THR C:13 , SER C:14 , GLY C:15 , ILE C:16 , GLY C:35 , PHE C:36 , ALA C:62 , ASP C:63 , LEU C:64 , ASN C:90 , ALA C:91 , 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 , HOH C:1087 , HOH C:1180 , HOH C:1242 , HOH C:1368 , HOH C:1420BINDING SITE FOR RESIDUE NAD C 300
5AC5SOFTWAREGLY 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 , SER D:65 , ASN D:90 , ALA D:141 , SER D:142 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , TRP D:187 , VAL D:188 , HOH D:1124 , HOH D:1466BINDING SITE FOR RESIDUE NAD D 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZTU)

(-) 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:235
 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 d2ztua_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztuA00 A:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....-------------------------............hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztu A   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVR-------------------------LLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-         -         -    |  220       230       240       250       260
                                                                                                                                                                                                                      189                       215                                             


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q5KST5_PSEFR | Q5KST5 from UniProtKB/TrEMBL  Length:260

    Alignment length:253
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   
         Q5KST5_PSEFR     8 VVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d2ztub_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2ztuB00 B:8-260 NAD(P)-bindin                     g Rossmann-like Domain                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh..........---------------------........hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...-------------------------.............hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztu B   8 VVTGSTSGIGLGIATALAAQGADIVLNGF---------------------LYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWV-------------------------ELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    17        27        |-         -         -|       67        77        87        97       107       117       127       137       147       157       167       177       187|        -         -      |217       227       237       247       257   
                                                       36                    58                                                                                                                               188                       214                                              


Chain C from PDB  Type:PROTEIN  Length:242
 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 d2ztuc_ C: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztuC00 C:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....------------------hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztu C   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVR------------------QETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-         -       210       220       230       240       250       260
                                                                                                                                                                                                                      189                208                                                    


Chain D from PDB  Type:PROTEIN  Length:241
 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 d2ztud_ D: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztuD00 D:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----adh_short-2ztuD01 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----adh_short-2ztuD02 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----adh_short-2ztuD03 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----adh_short-2ztuD04 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....-------------------hhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztu D   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVR-------------------ETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-         -       210       220       230       240       250       260
                                                                                                                                                                                                                      189                 209
   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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  2ztu
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1wmb THE WILD-TYPE ENZYME WITH THE OPEN CONFORMATION
1x1t THE WILD-TYPE ENZYME COMPLEXED WITH NAD+
2ztl THE TERNAY COMPLEX OF THE WILD-TYPE ENZYME WITH THE CLOSED CONFORMATION
2ztm T190S MUTANT ENZYME
2ztv