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(-) Description

Title :  CRYSTAL STRUCTURE OF L-ASPARTATE DEHYDROGENASE FROM HYPERTHERMOPHILIC ARCHAEON ARCHAEOGLOBUS FULGIDUS
 
Authors :  K. Yoneda, H. Sakuraba, H. Tsuge, T. Ohshima
Date :  19 Dec 05  (Deposition) - 26 Dec 06  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Aspartate Dehydrogenase, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yoneda, H. Sakuraba, H. Tsuge, N. Katunuma, T. Ohshima
Crystal Structure Of Archaeal Highly Thermostable L-Aspartate Dehydrogenase/Nad/Citrate Ternary Complex.
Febs J. V. 274 4315 2007
PubMed-ID: 17651440  |  Reference-DOI: 10.1111/J.1742-4658.2007.05961.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:111 , ASN A:160 , LEU A:161 , ASN A:162 , VAL A:163 , HIS A:189 , LYS A:214 , THR A:215 , SER A:216 , NAD A:242 , HOH A:1623 , HOH A:1627BINDING SITE FOR RESIDUE CIT A 1585
2AC2SOFTWAREALA B:1111 , LYS B:1134 , ASN B:1160 , LEU B:1161 , ASN B:1162 , VAL B:1163 , ASN B:1187 , HIS B:1189 , LYS B:1214 , SER B:1216 , NAD B:1242BINDING SITE FOR RESIDUE CIT B 2585
3AC3SOFTWAREGLY A:7 , GLY A:9 , ALA A:10 , ILE A:11 , ASP A:31 , VAL A:32 , ALA A:58 , SER A:59 , ALA A:62 , TYR A:66 , LEU A:80 , SER A:81 , GLY A:110 , ALA A:111 , ASN A:162 , ASN A:212 , THR A:215 , ALA A:219 , CIT A:1585 , HOH A:1590 , HOH A:1597 , HOH A:1599 , HOH A:1644 , HOH A:1652BINDING SITE FOR RESIDUE NAD A 242
4AC4SOFTWAREHOH B:5 , HOH B:26 , HOH B:38 , HOH B:119 , HOH B:125 , GLY B:1007 , GLY B:1009 , ALA B:1010 , ILE B:1011 , ARG B:1021 , ASP B:1031 , VAL B:1032 , ARG B:1033 , ALA B:1058 , SER B:1059 , ALA B:1062 , TYR B:1066 , LEU B:1080 , SER B:1081 , GLY B:1110 , ALA B:1111 , ASN B:1162 , VAL B:1163 , ASN B:1212 , THR B:1215 , ALA B:1219 , CIT B:2585BINDING SITE FOR RESIDUE NAD B 1242

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DC1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DC1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DC1)

(-) Exons   (0, 0)

(no "Exon" information available for 2DC1)

(-) 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:236
 aligned with ASPD_ARCFU | O28440 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
          ASPD_ARCFU      1 MLVGLIGYGAIGKFLAEWLERNGFEIAAILDVRGEHEKMVRGIDEFLQREMDVAVEAASQQAVKDYAEKILKAGIDLIVLSTGAFADRDFLSRVREVCRKTGRRVYIASGAIGGLDAIFSASELIEEIVLTTRKNWRQFGRKGVIFEGSASEAAQKFPKNLNVAATLSIASGKDVKVRLVADEVEENIHEILVRGEFGEMEIRVRNRPMRENPKTSYLAALSVTRILRNLKEGLVV  236
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dc1A01 A:1-110,A:212-236 NAD(P)-binding Rossmann-like Domain                                                 2dc1A02 A:111-211 Dihydrodipicolinate Reductase; domain 2                                            2dc1A01 A:1-110,A:212-236 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeeee........ee.hhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhh...eeeeeeeeeee.hhh...eeeeeeehhhhhhhh...hhhhhhhhhhhh...eeeeeee....eeeeeeeee..eeeeeeeee.ee..eeeeehhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2dc1 A    1 MLVGLIGYGAIGKFLAEWLERNGFEIAAILDVRGEHEKMVRGIDEFLQREMDVAVEAASQQAVKDYAEKILKAGIDLIVLSTGAFADRDFLSRVREVCRKTGRRVYIASGAIGGLDAIFSASELIEEIVLTTRKNWRQFGRKGVIFEGSASEAAQKFPKNLNVAATLSIASGKDVKVRLVADEVEENIHEILVRGEFGEMEIRVRNRPMRENPKTSYLAALSVTRILRNLKEGLVV  236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      


Chain B from PDB  Type:PROTEIN  Length:236
 aligned with ASPD_ARCFU | O28440 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
          ASPD_ARCFU      1 MLVGLIGYGAIGKFLAEWLERNGFEIAAILDVRGEHEKMVRGIDEFLQREMDVAVEAASQQAVKDYAEKILKAGIDLIVLSTGAFADRDFLSRVREVCRKTGRRVYIASGAIGGLDAIFSASELIEEIVLTTRKNWRQFGRKGVIFEGSASEAAQKFPKNLNVAATLSIASGKDVKVRLVADEVEENIHEILVRGEFGEMEIRVRNRPMRENPKTSYLAALSVTRILRNLKEGLVV  236
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dc1B01 B:1001-1110,B:1212-1236 NAD(P)-binding Rossmann-like Domain                                           2dc1B02 B:1111-1211 Dihydrodipicolinate Reductase; domain 2                                          2dc1B01                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeeee........ee.hhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhh...eeeeeeeeeee.hhhh..eeeeeeehhhhhhhh...hhhhhhhhhhhh...eeeeeee.....eeeeeeee..eeeeeeee..ee..eeeeehhhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2dc1 B 1001 MLVGLIGYGAIGKFLAEWLERNGFEIAAILDVRGEHEKMVRGIDEFLQREMDVAVEAASQQAVKDYAEKILKAGIDLIVLSTGAFADRDFLSRVREVCRKTGRRVYIASGAIGGLDAIFSASELIEEIVLTTRKNWRQFGRKGVIFEGSASEAAQKFPKNLNVAATLSIASGKDVKVRLVADEVEENIHEILVRGEFGEMEIRVRNRPMRENPKTSYLAALSVTRILRNLKEGLVV 1236
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230
   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 2DC1)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DC1)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ASPD_ARCFU | O28440)
molecular function
    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:0033735    aspartate dehydrogenase activity    Catalysis of the reaction: L-aspartate + H2O + NAD(P)+ = oxaloacetate + NH3 + NAD(P)H + 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.
    GO:0016639    oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0006742    NADP catabolic process    The chemical reactions and pathways resulting in the breakdown of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; catabolism may be of either the oxidized form, NADP, or the reduced form, NADPH.
    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:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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