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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A HOMOSERINE DEHYDROGENASE FROM THIOBACILLUS DENITRIFICANS TO 2.15A
 
Authors :  A. J. Stein, H. Cui, S. Chin, A. Savchenko, A. Joachimiak, Midwest Cent Structural Genomics (Mcsg)
Date :  30 Apr 10  (Deposition) - 12 May 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (1x)
Keywords :  Rossmann-Fold, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Stein, H. Cui, S. Chin, A. Savchenko, A. Joachimiak
The Crystal Structure Of A Homoserine Dehydrogenase From Thiobacillus Denitrificans To 2. 15A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HOMOSERINE DEHYDROGENASE
    ChainsA
    EC Number1.1.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET DERIVATIVE
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTBD_0843
    Organism ScientificTHIOBACILLUS DENITRIFICANS
    Organism Taxid292415
    StrainATCC 25259

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 48)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE
2SO412Ligand/IonSULFATE ION
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:35 , HIS A:320 , HOH A:543BINDING SITE FOR RESIDUE SO4 A 438
2AC2SOFTWAREGLN A:119 , HIS A:326 , PRO A:329 , HIS A:330 , LEU A:331 , GLN A:334 , HOH A:469 , HOH A:505 , HOH A:510 , HOH A:527BINDING SITE FOR RESIDUE SO4 A 439
3AC3SOFTWAREARG A:252 , ALA A:254 , GLU A:255 , ARG A:350 , HOH A:473BINDING SITE FOR RESIDUE SO4 A 440

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MTJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3MTJ)

(-) 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:431
 aligned with Q3SKI5_THIDA | Q3SKI5 from UniProtKB/TrEMBL  Length:437

    Alignment length:438
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                               |     7        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       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427        
         Q3SKI5_THIDA     - ---MKPIHVGLLGLGTVGGGTLTVLRRNAEEITRRAGREIRVVRAAVRNLDKAEALAGGLPLTTNPFDVVDDPEIDIVVELIGGLEPARELVMQAIANGKHVVTANKHLVAKYGNEIFAAAQAKGVMVTFEAAVAGGIPIIKALREGLTANRIEWLAGIINGTSNFILSEMRDKGAAFDDVLKEAQRLGYAEADPTFDIEGIDAAHKLTILSAIAFGIPMQFERAYTEGISQLTREDVRYAEELGYRIKLLGIARRAENGIELRVHPTLIPERRLIANVDGAMNAVLVKGDAVGPTLYYGAGAGSEPTASAVVADLVDVTRLHTADPHHRVPHLAFQPDQLADTPILPMEAVRTAYYLRLRAFDRPGVLADITRILADSSISIDAMVQKEPAEGEEQVDIILLTHVTLEKNVNAAIAKIEALDAVAGKVMRIRLEDLG 435
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------NAD_binding_3-3mtjA02 A:10-128                                                                                         -------Homoserine_dh-3mtjA03 A:136-314                                                                                                                                                    --------------------------------------ACT-3mtj A01 A:353-421                                               -------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh...ee..hhhhhh.....eeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh..eehhhhh....hhhhhhhh......eeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee......hhhhhhhhhhhheeeeeeeeeee....eeeeeeeeeee...hhhhh...eeeeeeee...eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......hhhh.eeeeeeeeee.-.hhhhhhhhhhhhhh...eeeeee.------..eeeeeee..eehhhhhhhhhhhh.........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mtj A  -2 FQGmKPIHVGLLGLGTVGGGTLTVLRRNAEEITRRAGREIRVVRAAVRNLDKAEALAGGLPLTTNPFDVVDDPEIDIVVELIGGLEPARELVmQAIANGKHVVTANKHLVAKYGNEIFAAAQAKGVmVTFEAAVAGGIPIIKALREGLTANRIEWLAGIINGTSNFILSEmRDKGAAFDDVLKEAQRLGYAEADPTFDIEGIDAAHKLTILSAIAFGIPmQFERAYTEGISQLTREDVRYAEELGYRIKLLGIARRAENGIELRVHPTLIPERRLIANVDGAmNAVLVKGDAVGPTLYYGAGAGSEPTASAVVADLVDVTRLHTADPHHRVPHLAFQPDQLADTPILPmEAVRTAYYLRLRAF-RPGVLADITRILADSSISIDAmVQK------EQVDIILLTHVTLEKNVNAAIAKIEALDAVAGKVmRIRLEDLG 435
                               |     7        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       267       277  |    287       297       307       317       327       337       347       357  | |  367       377     |  |-     | 397       407       417       427        
                               |                                                                                       90-MSE                           124-MSE                                     168-MSE                                          217-MSE                                                        280-MSE                                                           346-MSE       360 |                  383-MSE   393                               427-MSE    
                               1-MSE                                                                                                                                                                                                                                                                                                                                                                  362                     386                                                 

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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  (0, 0)

(no "SCOP Domain" information available for 3MTJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: ACT (34)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q3SKI5_THIDA | Q3SKI5)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0004412    homoserine dehydrogenase activity    Catalysis of the reaction: L-homoserine + NADP+ = L-aspartate-4-semialdehyde + NADPH + H+.
    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:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    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:0009088    threonine biosynthetic process    The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

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