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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMOSERINE DEHYDROGENASE FROM THERMOPLASMA VOLCANIUM
 
Authors :  J. Osipiuk, R. Hendricks, J. Abdullah, A. Joachimiak, Midwest Center Structural Genomics (Mcsg)
Date :  12 Feb 08  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Apc89447, Homoserine, Dehydrogenase, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, R. Hendricks, J. Abdullah, A. Joachimiak
X-Ray Crystal Structure Of Homoserine Dehydrogenase From Thermoplasma Volcanium.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HOMOSERINE DEHYDROGENASE
    Atcc: 51530
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TVG0375766, TV0389
    Organism Scientific: THERMOPLASMA VOLCANIUM GSS1
    Organism Taxid: 273116
    Strain: GSS1 / DSM 4299 / IFO 15438 / JCM 9571

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , ILE A:52 , ASP A:53 , ILE A:54 , GLY A:55 , HOH A:520 , HOH A:576BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREARG A:187 , HOH A:455 , HOH A:722BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREASP A:214 , LYS A:218 , HOH A:425 , HOH A:479 , HOH A:529BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREARG A:232BINDING SITE FOR RESIDUE SO4 A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C8M)

(-) Exons   (0, 0)

(no "Exon" information available for 3C8M)

(-) 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:324
 aligned with Q97BR6_THEVO | Q97BR6 from UniProtKB/TrEMBL  Length:328

    Alignment length:325
                                    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       300       310       320     
         Q97BR6_THEVO     1 MKTINLSIFGLGNVGLNLLRIIRSFNEENRLGLKFNVVFVADSLHSYYNERIDIGKVISYKEKGSLDSLEYESISASEALARDFDIVVDATPASADGKKELAFYKETFENGKDVVTANKSGLANFWPEIMEYARSNNRRIRYEATVAGGVPLFSFIDYSVLPSRIKKFRGIVSLTINYFIRELANKREFDDVLSEATKLGIVEKNYKDDLTGLDAARKSVILCNHLYGSSYRLSDVFYEGILDQDRSFGKNERLVTETGIVNGKPSAESRIKSLDSNDYLLTLGKGSLGYQLQTDTNGTLNVSDLYDGPYETAGAVMNDLVILSM 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3c8mA01 A:2-150,A:306-324 NAD(P)-binding Rossmann-like Domain                                                                                        3c8mA02 A:151-305 Dihydrodipicolinate Reductase; domain 2                                                                                                  3c8mA01            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhhh...eeeeeeeee....eee....hhhhhhhhhhh.hhhhh..ee.hhhhhhhh...eeee.......hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..eehhhhh.....hhhhhhhhh......eeeee.hhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhee....-........eeeeeeeeee..eeeeeeeeee....hhhhhh.....eeeee.....eeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8m A   1 mKTINLSIFGLGNVGLNLLRIIRSFNEENRLGLKFNVVFVADSLHSYYNERIDIGKVISYKEKGSLDSLEYESISASEALARDFDIVVDATPASADGKKELAFYKETFENGKDVVTANKSGLANFWPEImEYARSNNRRIRYEATVAGGVPLFSFIDYSVLPSRIKKFRGIVSLTINYFIRELANKREFDDVLSEATKLGIVEKNYKDDLTGLDAARKSVILCNHLYGSSYRLSDVFYEGIL-QDRSFGKNERLVTETGIVNGKPSAESRIKSLDSNDYLLTLGKGSLGYQLQTDTNGTLNVSDLYDGPYETAGAVmNDLVILSm 325
                            |       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       300       310      |320    |
                            |                                                                                                                              130-MSE                                                                                                         242 |                                                                      317-MSE 325-MSE
                            1-MSE                                                                                                                                                                                                                                            244
   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  (0, 0)

(no "SCOP Domain" information available for 3C8M)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C8M)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q97BR6_THEVO | Q97BR6)
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:0004412    homoserine dehydrogenase activity    Catalysis of the reaction: L-homoserine + NADP+ = L-aspartate-4-semialdehyde + NADPH + H+.
    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: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: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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