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(-) Description

Title :  CRYSTAL STRUCTURE OF A SERINE DEHYDROGENASE FROM PSEUDOMONAS AERUGINOSA PAO1 IN COMPLEX WITH NAD
 
Authors :  K. Tan, A. U. Singer, E. Evdokimova, M. Kudritska, A. Savchenko, A. M. Ed A. Joachimiak, A. F. Yakunin, Midwest Center For Structural Geno (Mcsg)
Date :  21 Dec 10  (Deposition) - 23 Feb 11  (Release) - 01 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Fold, Oxidoreductase (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
    Chains: A
    EC Number: 1.1.1.276
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P11
    Expression System Strain: BL21 CODONPLUS(DE3)-RP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PA0743
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PA01

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 56)
No.NameCountTypeFull Name
1MSE52Mod. Amino AcidSELENOMETHIONINE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:7 , GLY A:8 , LEU A:9 , GLY A:10 , HIS A:11 , MSE A:12 , PHE A:30 , ASP A:31 , LEU A:32 , MSE A:64 , LEU A:65 , PRO A:66 , THR A:96 , VAL A:121 , GLY A:123 , LYS A:171 , PHE A:239 , LYS A:246 , ASP A:247 , HOH A:307 , HOH A:322 , HOH A:330BINDING SITE FOR RESIDUE NAD A 299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q3C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q3C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q3C)

(-) 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

(-) Exons   (0, 0)

(no "Exon" information available for 3Q3C)

(-) 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:294
 aligned with SERDH_PSEAE | Q9I5I6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:295
                                    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       291     
          SERDH_PSEAE     2 KQIAFIGLGHMGAPMATNLLKAGYLLNVFDLVQSAVDGLVAAGASAARSARDAVQGADVVISMLPASQHVEGLYLDDDGLLAHIAPGTLVLECSTIAPTSARKIHAAARERGLAMLDAPVSGGTAGAAAGTLTFMVGGDAEALEKARPLFEAMGRNIFHAGPDGAGQVAKVCNNQLLAVLMIGTAEAMALGVANGLEAKVLAEIMRRSSGGNWALEVYNPWPGVMENAPASRDYSGGFMAQLMAKDLGLAQEAAQASASSTPMGSLALSLYRLLLKQGYAERDFSVVQKLFDPTQ 296
               SCOP domains d3q3ca1 A:2-162 Hydroxyisobutyrate dehydrogenase                                                                                                                 d3q3ca2 A:163-296 Hydroxyisobutyrate dehydrogenase                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhh..ee..hhhhhhh...eeee...hhhhhhhhhh.-.hhhhhh....eeee....hhhhhhhhhhhhhh...eeee..ee.hhhhhhhh.eeeeee.hhhhhhhhhhhhhhheeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhh.........hhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----3_HYDROXYISOBU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q3c A   2 KQIAFIGLGHmGAPmATNLLKAGYLLNVFDLVQSAVDGLVAAGASAARSARDAVQGADVVISmLPASQHVEGLYLD-DGLLAHIAPGTLVLECSTIAPTSARKIHAAARERGLAmLDAPVSGGTAGAAAGTLTFmVGGDAEALEKARPLFEAmGRNIFHAGPDGAGQVAKVCNNQLLAVLmIGTAEAmALGVANGLEAKVLAEImRRSSGGNWALEVYNPWPGVmENAPASRDYSGGFmAQLmAKDLGLAQEAAQASASSTPmGSLALSLYRLLLKQGYAERDFSVVQKLFDPTQ 296
                                    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       291     
                                     12-MSE                                              64-MSE       77 |                                  116-MSE             136-MSE           154-MSE                     182-MSE  |              206-MSE             226-MSE       240-MSE                 264-MSE                            
                                         16-MSE                                                         79                                                                                                           189-MSE                                                244-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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q3C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q3C)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        SERDH_PSEAE | Q9I5I6: 3obb

(-) Related Entries Specified in the PDB File

3obb CRYSTAL STRUCTURE OF A POSSIBLE 3-HYDROXYISOBUTYRATE DEHYDROGENASE FROM PSEUDOMONAS AERUGINOSA PAO1 RELATED ID: APC6014 RELATED DB: TARGETDB