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(-) Description

Title :  CRYSTAL STRUCTURE OF A POSSIBLE 3-HYDROXYISOBUTYRATE DEHYDROGENASE FROM PSEUDOMONAS AERUGINOSA PAO1
 
Authors :  K. Tan, A. U. Singer, E. Evdokimova, M. Kudritska, A. Savchenko, A. M. Ed A. F. Yakunin, A. Joachimiak, Midwest Center For Structural Geno (Mcsg)
Date :  06 Aug 10  (Deposition) - 18 Aug 10  (Release) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase, Alpha-Beta, Serine Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Tchigvintsev, A. Singer, G. Brown, R. Flick, E. Evdokimova, K. Tan, C. F. Gonzalez, A. Savchenko, A. F. Yakunin
Biochemical And Structural Studies Of Uncharacterized Protein Pa0743 From Pseudomonas Aeruginosa Revealed Nad+-Dependent L-Serine Dehydrogenase.
J. Biol. Chem. V. 287 1874 2012
PubMed-ID: 22128181  |  Reference-DOI: 10.1074/JBC.M111.294561

(-) Compounds

Molecule 1 - PROBABLE 3-HYDROXYISOBUTYRATE DEHYDROGENASE
    ChainsA
    EC Number1.1.1.276
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP11
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePA0743
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    StrainPA01

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A
Biological Unit 2 (2x)A
Biological Unit 3 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 76)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3EPE4Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MSE56Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (4, 38)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (4, 38)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , MSE A:12 , PHE A:239BINDING SITE FOR RESIDUE ACT A 402
2AC2SOFTWAREASP A:38 , GLN A:242 , LEU A:276 , HOH A:551 , HOH A:555BINDING SITE FOR RESIDUE ACT A 403
3AC3SOFTWAREARG A:233 , SER A:236 , GLY A:237 , GLY A:238BINDING SITE FOR RESIDUE ACT A 404
4AC4SOFTWAREGLY A:10 , HIS A:11BINDING SITE FOR RESIDUE EDO A 405
5AC5SOFTWAREVAL A:121 , GLY A:123 , GLY A:124 , LYS A:171 , ASN A:175 , TRP A:214 , TYR A:219 , PHE A:239 , ASP A:247 , HOH A:570BINDING SITE FOR RESIDUE EPE A 299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OBB)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:80 -Leu A:81
2Ala A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OBB)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
13_HYDROXYISOBUT_DHPS00895 3-hydroxyisobutyrate dehydrogenase signature.SERDH_PSEAE6-19  1A:6-19
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
13_HYDROXYISOBUT_DHPS00895 3-hydroxyisobutyrate dehydrogenase signature.SERDH_PSEAE6-19  4A:6-19
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
13_HYDROXYISOBUT_DHPS00895 3-hydroxyisobutyrate dehydrogenase signature.SERDH_PSEAE6-19  2A:6-19
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
13_HYDROXYISOBUT_DHPS00895 3-hydroxyisobutyrate dehydrogenase signature.SERDH_PSEAE6-19  2A:6-19

(-) Exons   (0, 0)

(no "Exon" information available for 3OBB)

(-) Sequences/Alignments

Asymmetric 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:295
 aligned with SERDH_PSEAE | Q9I5I6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:296
                                    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       290      
          SERDH_PSEAE     1 MKQIAFIGLGHMGAPMATNLLKAGYLLNVFDLVQSAVDGLVAAGASAARSARDAVQGADVVISMLPASQHVEGLYLDDDGLLAHIAPGTLVLECSTIAPTSARKIHAAARERGLAMLDAPVSGGTAGAAAGTLTFMVGGDAEALEKARPLFEAMGRNIFHAGPDGAGQVAKVCNNQLLAVLMIGTAEAMALGVANGLEAKVLAEIMRRSSGGNWALEVYNPWPGVMENAPASRDYSGGFMAQLMAKDLGLAQEAAQASASSTPMGSLALSLYRLLLKQGYAERDFSVVQKLFDPTQ 296
               SCOP domains d3obba2 A:1-162 Hydroxyisobutyrate dehydrogenase                                                                                                                  d3obba1 A:163-296 Hydroxyisobutyrate dehydrogenase                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee..hhhhhhh...eeee...hhhhhhhhhhh..........-.eeee....hhhhhhhhhhhhhh...eeee..ee.hhhhhhhh.eeeeee.hhhhhhhhhhhhhhheeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----3_HYDROXYISOBU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3obb A   1 mKQIAFIGLGHmGAPmATNLLKAGYLLNVFDLVQSAVDGLVAAGASAARSARDAVQGADVVISmLPASQHVEGLYLDDDGLLAHIAP-TLVLECSTIAPTSARKIHAAARERGLAmLDAPVSGGTAGAAAGTLTFmVGGDAEALEKARPLFEAmGRNIFHAGPDGAGQVAKVCNNQLLAVLmIGTAEAmALGVANGLEAKVLAEImRRSSGGNWALEVYNPWPGVmENAPASRDYSGGFmAQLmAKDLGLAQEAAQASASSTPmGSLALSLYRLLLKQGYAERDFSVVQKLFDPTQ 296
                            |       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       290      
                            |         12-MSE                                              64-MSE                 87 |                        116-MSE             136-MSE           154-MSE                     182-MSE  |              206-MSE             226-MSE       240-MSE                 264-MSE                            
                            1-MSE         16-MSE                                                                   89                                                                                                 189-MSE                                                244-MSE                                                

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 3CUM: 1,1)

(no "CATH Domain" information available for 3OBB, only for superseded entry 3CUM replaced by 3OBB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OBB)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SERDH_PSEAE | Q9I5I6)
molecular function
    GO:0008442    3-hydroxyisobutyrate dehydrogenase activity    Catalysis of the reaction: 3-hydroxy-2-methylpropanoate + NAD+ = 2-methyl-3-oxopropanoate + NADH + H+.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    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:0006565    L-serine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0009083    branched-chain amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    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.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

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        SERDH_PSEAE | Q9I5I63q3c

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