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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTATE SEMIALDEHYDE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  W. Kagawa, N. Fujikawa, H. Kurumizaka, Y. Bessho, M. J. Ellis, S. V. Anto R. W. Strange, S. S. Hasnain, S. Kuramitsu, S. Yokoyama, Riken Struct Genomics/Proteomics Initiative (Rsgi)
Date :  07 Apr 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Aspartate Pathway, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Kagawa, N. Fujikawa, H. Kurumizaka, Y. Bessho, M. J. Ellis, S. V. Antonyuk, R. W. Strange, S. S. Hasnain, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Aspartate Semialdehyde Dehydrogenase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YV3)

(-) Sites  (0, 0)

(no "Site" information available for 2YV3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YV3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:60 -Pro A:61
2Leu B:60 -Pro B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YV3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YV3)

(-) Exons   (0, 0)

(no "Exon" information available for 2YV3)

(-) 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:328
 aligned with Q5SKU8_THET8 | Q5SKU8 from UniProtKB/TrEMBL  Length:331

    Alignment length:328
                                    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        
         Q5SKU8_THET8     1 MRVAVVGATGAVGREILKVLEARNFPLSELRLYASPRSAGVRLAFRGEEIPVEPLPEGPLPVDLVLASAGGGISRAKALVWAEGGALVVDNSSAWRYEPWVPLVVPEVNREKIFQHRGIIANPNCTTAILAMALWPLHRAFQAKRVIVATYQAASGAGAKAMEELLTETHRFLHGEAPKAEAFAHPLPFNVIPHIDAFQENGYTREEMKVVWETHKIFGDDTIRISATAVRVPTLRAHAEAVSVEFARPVTPEAAREVLKEAPGVEVVDEPEAKRYPMPLTASGKWDVEVGRIRKSLAFENGLDFFVVGDQLLKGAALNAVQIAEEWL 328
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhh.......eeeehhhhh..eeee..eeeeeee.........eeee.hhhhhhhhhhhhhhhh..eeee..................hhhhhhhh..eee..hhhhhhhhhhhhhhhhhhheeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhh.....eeeee........eeeeeeeeee....hhhhhhhhhh.................hhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv3 A   1 MRVAVVGATGAVGREILKVLEARNFPLSELRLYASPRSAGVRLAFRGEEIPVEPLPEGPLPVDLVLASAGGGISRAKALVWAEGGALVVDNSSAWRYEPWVPLVVPEVNREKIFQHRGIIANPNCTTAILAMALWPLHRAFQAKRVIVATYQAASGAGAKAMEELLTETHRFLHGEAPKAEAFAHPLPFNVIPHIDAFQENGYTREEMKVVWETHKIFGDDTIRISATAVRVPTLRAHAEAVSVEFARPVTPEAAREVLKEAPGVEVVDEPEAKRYPMPLTASGKWDVEVGRIRKSLAFENGLDFFVVGDQLLKGAALNAVQIAEEWL 328
                                    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        


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with Q5SKU8_THET8 | Q5SKU8 from UniProtKB/TrEMBL  Length:331

    Alignment length:328
                                    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        
         Q5SKU8_THET8     1 MRVAVVGATGAVGREILKVLEARNFPLSELRLYASPRSAGVRLAFRGEEIPVEPLPEGPLPVDLVLASAGGGISRAKALVWAEGGALVVDNSSAWRYEPWVPLVVPEVNREKIFQHRGIIANPNCTTAILAMALWPLHRAFQAKRVIVATYQAASGAGAKAMEELLTETHRFLHGEAPKAEAFAHPLPFNVIPHIDAFQENGYTREEMKVVWETHKIFGDDTIRISATAVRVPTLRAHAEAVSVEFARPVTPEAAREVLKEAPGVEVVDEPEAKRYPMPLTASGKWDVEVGRIRKSLAFENGLDFFVVGDQLLKGAALNAVQIAEEWL 328
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Semialdhyde_dh-2yv3B03 B:2-116                                                                                     -----------------Semialdhyde_dhC-2yv3B01 B:134-314                                                                                                                                                    -------------- Pfam domains (1)
           Pfam domains (2) -Semialdhyde_dh-2yv3B04 B:2-116                                                                                     -----------------Semialdhyde_dhC-2yv3B02 B:134-314                                                                                                                                                    -------------- Pfam domains (2)
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh.....eeeeeehhhhh..eeee..eeeeeee.........eeee...hhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh...eee..eeee.hhhhh.hhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhh.......ee........eeeeeeeeee....hhhhhhhhhh....eee..hhhhh.............eeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yv3 B   1 MRVAVVGATGAVGREILKVLEARNFPLSELRLYASPRSAGVRLAFRGEEIPVEPLPEGPLPVDLVLASAGGGISRAKALVWAEGGALVVDNSSAWRYEPWVPLVVPEVNREKIFQHRGIIANPNCTTAILAMALWPLHRAFQAKRVIVATYQAASGAGAKAMEELLTETHRFLHGEAPKAEAFAHPLPFNVIPHIDAFQENGYTREEMKVVWETHKIFGDDTIRISATAVRVPTLRAHAEAVSVEFARPVTPEAAREVLKEAPGVEVVDEPEAKRYPMPLTASGKWDVEVGRIRKSLAFENGLDFFVVGDQLLKGAALNAVQIAEEWL 328
                                    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
   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 2YV3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YV3)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GADPH_aa-bio_dh (59)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SKU8_THET8 | Q5SKU8)
molecular function
    GO:0003942    N-acetyl-gamma-glutamyl-phosphate reductase activity    Catalysis of the reaction: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetyl-5-glutamyl phosphate + NADPH + 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: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:0004073    aspartate-semialdehyde dehydrogenase activity    Catalysis of the reaction: L-aspartate 4-semialdehyde + NADP(+) + phosphate = 4-phospho-L-aspartate + H(+) + NADPH.
    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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0071266    'de novo' L-methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid, from simpler components.
    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:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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