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(-) Description

Title :  CLOSED CONFORMATION OF D-3-HYDROXYBUTYRATE DEHYDROGENASE COMPLEXED WITH NAD+ AND L-3-HYDROXYBUTYRATE
 
Authors :  K. Nakashima, Y. Nakajima, K. Ito, T. Yoshimoto
Date :  07 Oct 08  (Deposition) - 25 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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

(-) 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
    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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
13HL4Ligand/Ion(3S)-3-HYDROXYBUTANOIC ACID
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , TRP A:187 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , 3HL A:301 , HOH A:1041 , HOH A:1216 , HOH A:1253 , HOH A:1401 , HOH A:1783BINDING SITE FOR RESIDUE NAD A 300
02AC2SOFTWAREGLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , TRP A:187 , LEU A:192 , GLN A:196 , NAD A:300BINDING SITE FOR RESIDUE 3HL A 301
03AC3SOFTWAREARG A:260 , HOH A:410 , ARG D:260 , HOH D:407 , HOH D:408 , HOH D:409BINDING SITE FOR RESIDUE MG A 406
04AC4SOFTWAREGLY B:11 , THR B:13 , SER B:14 , ILE B:16 , ASN B:34 , GLY B:35 , PHE B:36 , ALA B:62 , ASP B:63 , LEU B:64 , ASN B:90 , GLY B:92 , LEU B:113 , ILE B:140 , ALA B:141 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , TRP B:187 , VAL B:188 , THR B:190 , PRO B:191 , VAL B:193 , 3HL B:301 , HOH B:1169 , HOH B:1766BINDING SITE FOR RESIDUE NAD B 300
05AC5SOFTWAREGLN B:94 , SER B:142 , HIS B:144 , LYS B:152 , TYR B:155 , LEU B:192 , GLN B:196 , NAD B:300BINDING SITE FOR RESIDUE 3HL B 301
06AC6SOFTWAREARG B:260 , HOH B:402 , HOH B:405 , ARG C:260 , HOH C:403 , HOH C:404BINDING SITE FOR RESIDUE MG B 401
07AC7SOFTWAREGLY 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 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , TRP C:187 , VAL C:188 , THR C:190 , PRO C:191 , LEU C:192 , VAL C:193 , 3HL C:301 , HOH C:1024 , HOH C:1091 , HOH C:1301 , HOH C:1313 , HOH C:1433 , HOH C:1640BINDING SITE FOR RESIDUE NAD C 300
08AC8SOFTWAREGLN C:94 , SER C:142 , HIS C:144 , LYS C:152 , TYR C:155 , TRP C:187 , LEU C:192 , GLN C:196 , NAD C:300BINDING SITE FOR RESIDUE 3HL C 301
09AC9SOFTWAREGLY 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 , GLY D:92 , LEU D:113 , ILE D:140 , ALA D:141 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , TRP D:187 , VAL D:188 , THR D:190 , PRO D:191 , LEU D:192 , VAL D:193 , 3HL D:301 , HOH D:1036 , HOH D:1068 , HOH D:1226 , HOH D:1406 , HOH D:1614 , HOH D:1792BINDING SITE FOR RESIDUE NAD D 300
10BC1SOFTWAREGLN D:94 , SER D:142 , HIS D:144 , LYS D:152 , TYR D:155 , LEU D:192 , GLN D:196 , NAD D:300BINDING SITE FOR RESIDUE 3HL D 301
11BC2SOFTWARELYS C:3 , LYS C:5 , ARG C:83 , HOH C:1103 , HOH C:1803 , TYR D:59 , GLY D:61 , HOH D:1100 , HOH D:1292 , HOH D:1335BINDING SITE FOR RESIDUE GOL D 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZTL)

(-) 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:260
 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 d2ztla_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztlA00 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.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztl A   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 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


Chain B from PDB  Type:PROTEIN  Length:260
 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 d2ztlb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztlB00 B: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....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztl B   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 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


Chain C from PDB  Type:PROTEIN  Length:260
 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 d2ztlc_ C: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztlC00 C:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztl C   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 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


Chain D from PDB  Type:PROTEIN  Length:260
 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 d2ztld_ D: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2ztlD00 D:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----adh_short-2ztlD01 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----adh_short-2ztlD02 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----adh_short-2ztlD03 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----adh_short-2ztlD04 D:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ztl D   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 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
   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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  2ztl
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  1.1.1.30
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1wmb THE SAME PROTEIN WITH THE OPEN CONFORMATION
1x1t THE SAME PROTEIN COMPLEXED WITH NAD+
2ztm