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(-) Description

Title :  STRUCTURE OF HYDROXYISOBUTYRATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. K. Lokanath, N. Kunishima, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 Jun 05  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydroxyisobutyrate, Valine Catabolism, Nadp+, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, N. Ohshima, K. Takio, I. Shiromizu, C. Kuroishi, N. Okazaki, S. Kuramitsu, S. Yokoyama, M. Miyano, N. Kunishima
Crystal Structure Of Novel Nadp-Dependent 3-Hydroxyisobutyrate Dehydrogenase From Thermus Thermophilu Hb8
J. Mol. Biol. V. 352 905 2005
PubMed-ID: 16126223  |  Reference-DOI: 10.1016/J.JMB.2005.07.068

(-) Compounds

Molecule 1 - 3-HYDROXYISOBUTYRATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1MSE21Mod. Amino AcidSELENOMETHIONINE
2NDP3Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:8 , LEU B:9 , GLY B:10 , ALA B:11 , MSE B:12 , ASN B:30 , ARG B:31 , THR B:32 , CYS B:62 , LEU B:63 , PRO B:64 , GLU B:68 , GLU B:71 , THR B:90 , SER B:91 , VAL B:116 , GLY B:119 , LYS B:165 , THR B:226 , PHE B:227 , LYS B:234 , HOH B:1311 , HOH B:1314 , HOH B:1315 , HOH B:1327 , HOH B:1328 , HOH B:1331 , HOH B:1351 , HOH B:1363 , HOH B:1375 , HOH B:1397 , HOH B:1468 , HOH B:1470 , HOH B:1482 , HOH B:1500 , HOH B:1510BINDING SITE FOR RESIDUE NDP B 1301
2AC2SOFTWAREGLY A:8 , LEU A:9 , GLY A:10 , ALA A:11 , MSE A:12 , ASN A:30 , ARG A:31 , THR A:32 , CYS A:62 , LEU A:63 , PRO A:64 , GLU A:68 , GLU A:71 , SER A:91 , VAL A:116 , GLY A:119 , LYS A:165 , THR A:226 , PHE A:227 , LYS A:234 , HOH A:1310 , HOH A:1311 , HOH A:1316 , HOH A:1321 , HOH A:1324 , HOH A:1353 , HOH A:1357 , HOH A:1363 , HOH A:1372 , HOH A:1390 , HOH A:1410 , HOH A:1417 , HOH A:1442 , HOH A:1445 , HOH A:1452 , HOH A:1525BINDING SITE FOR RESIDUE NDP A 1302
3AC3SOFTWAREGLY C:8 , LEU C:9 , GLY C:10 , ALA C:11 , MSE C:12 , ASN C:30 , ARG C:31 , THR C:32 , CYS C:62 , LEU C:63 , PRO C:64 , GLU C:68 , GLU C:71 , THR C:90 , SER C:91 , VAL C:116 , GLY C:119 , LYS C:165 , THR C:226 , PHE C:227 , LYS C:234 , HOH C:1321 , HOH C:1331 , HOH C:1333 , HOH C:1343 , HOH C:1351 , HOH C:1355 , HOH C:1371 , HOH C:1375 , HOH C:1410 , HOH C:1449 , HOH C:1463BINDING SITE FOR RESIDUE NDP C 1303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CVZ)

(-) 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:288
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
         Q5SLQ6_THET8     2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains d2cvza2 A:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d2cvza1 A:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 2cvzA01 A:2-157 NAD(P)-binding Rossmann-like Domain                                                                                                         2cvzA02 A:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhh...eeee...hhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh..eeeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cvz A   2 EKVAFIGLGAmGYPmAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVmLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAmGVLDGEKAPSPLLRLAREVYEmAKRELGPDADHVEALRLLERWGGVEIR 289
                                    11|   |   21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261|      271       281        
                                     12-MSE                                                                                                                131-MSE                                                                                                      240-MSE               262-MSE                       
                                         16-MSE                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:288
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
         Q5SLQ6_THET8     2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains d2cvzb2 B:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d2cvzb1 B:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 2cvzB01 B:2-157 NAD(P)-binding Rossmann-like Domain                                                                                                         2cvzB02 B:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhh...eeee...hhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh..eeeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cvz B   2 EKVAFIGLGAmGYPmAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVmLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAmGVLDGEKAPSPLLRLAREVYEmAKRELGPDADHVEALRLLERWGGVEIR 289
                                    11|   |   21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261|      271       281        
                                     12-MSE                                                                                                                131-MSE                                                                                                      240-MSE               262-MSE                       
                                         16-MSE                                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:289
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:289
                                    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       270       280         
         Q5SLQ6_THET8     1 MEKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains -d2cvzc2 C:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d2cvzc1 C:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains -2cvzC01 C:2-157 NAD(P)-binding Rossmann-like Domain                                                                                                         2cvzC02 C:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhh.eeee...hhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh...eeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cvz C   1 mEKVAFIGLGAmGYPmAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVmLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAmGVLDGEKAPSPLLRLAREVYEmAKRELGPDADHVEALRLLERWGGVEIR 289
                            |       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 |     270       280         
                            1-MSE     12-MSE                                                                                                                131-MSE                                                                                                      240-MSE               262-MSE                       
                                          16-MSE                                                                                                                                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:288
 aligned with Q5SLQ6_THET8 | Q5SLQ6 from UniProtKB/TrEMBL  Length:289

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
         Q5SLQ6_THET8     2 EKVAFIGLGAMGYPMAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVMLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAMGVLDGEKAPSPLLRLAREVYEMAKRELGPDADHVEALRLLERWGGVEIR 289
               SCOP domains d2cvzd2 D:2-157 Hydroxyisobutyrate dehydrogenase                                                                                                            d2cvzd1 D:158-289 Hydroxyisobutyrate dehydrogenase                                                                                   SCOP domains
               CATH domains 2cvzD01 D:2-157 NAD(P)-binding Rossmann-like Domain                                                                                                         2cvzD02 D:158-289 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh.eeee..hhhhhhhhhhhhh.ee.hhhhhhhh.eeee...hhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh..eeeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cvz D   2 EKVAFIGLGAmGYPmAGHLARRFPTLVWNRTFEKALRHQEEFGSEAVPLERVAEARVIFTCLPTTREVYEVAEALYPYLREGTYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEAGTLTVmLGGPEEAVERVRPFLAYAKKVVHVGPVGAGHAVKAINNALLAVNLWAAGEGLLALVKQGVSAEKALEVINASSGRSNATENLIPQRVLTRAFPKTFALGLLVKDLGIAmGVLDGEKAPSPLLRLAREVYEmAKRELGPDADHVEALRLLERWGGVEIR 289
                                    11|   |   21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261|      271       281        
                                     12-MSE                                                                                                                131-MSE                                                                                                      240-MSE               262-MSE                       
                                         16-MSE
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CVZ)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5SLQ6_THET8 | Q5SLQ6)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, 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.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
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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        Q5SLQ6_THET8 | Q5SLQ6: 1wp4

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