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(-) Description

Title :  ALANINE DEHYDROGENASE DIMER W/BOUND NAD (ARCHAEAL)
 
Authors :  D. T. Gallagher, N. N. Smith, M. J. Holden, I. Schroeder, H. G. Monbouquette
Date :  25 Feb 03  (Deposition) - 06 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Two-Domain, Beta-Sandwich-Dimer, Rossmann-Fold Nad Domain, Human Mu Crystallin Homolog, Human Thyroid-Hormone-Binder Homolog, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Gallagher, H. G. Monbouquette, I. Schroeder, H. Robinson, M. J. Holden, N. N. Smith
Structure Of Alanine Dehydrogenase From Archaeoglobus: Active Site Analysis And Relation To Bacterial Cyclodeaminases And Mammalian Mu Crystallin.
J. Mol. Biol. V. 342 119 2004
PubMed-ID: 15313611  |  Reference-DOI: 10.1016/J.JMB.2004.06.090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALANINE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: MZ1
    Expression System Taxid: 562
    Expression System Vector Type: PMHAF1
    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
1NA2Ligand/IonSODIUM ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:217 , ALA A:218 , GLU A:225 , GLU A:249BINDING SITE FOR RESIDUE NA A 900
2AC2SOFTWAREALA B:215 , GLY B:217 , ALA B:218 , GLU B:225 , GLU B:249BINDING SITE FOR RESIDUE NA B 901
3AC3SOFTWAREARG A:108 , THR A:109 , GLY A:134 , THR A:135 , GLN A:136 , TYR A:156 , ASP A:157 , VAL A:158 , ARG A:159 , THR A:195 , PRO A:196 , VAL A:201 , ILE A:216 , GLY A:217 , ASP A:219 , LYS A:223 , SER A:290 , THR A:291 , GLY A:292 , HOH A:579 , HOH A:658BINDING SITE FOR RESIDUE NAD A 400
4AC4SOFTWAREARG B:108 , THR B:109 , GLY B:132 , GLY B:134 , THR B:135 , GLN B:136 , TYR B:156 , ASP B:157 , VAL B:158 , ARG B:159 , THR B:194 , THR B:195 , PRO B:196 , VAL B:201 , ILE B:216 , GLY B:217 , ASP B:219 , LYS B:223 , SER B:290 , THR B:291 , GLY B:292 , HOH B:670 , HOH B:684 , HOH B:692 , HOH B:760BINDING SITE FOR RESIDUE NAD B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OMO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OMO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OMO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OMO)

(-) Exons   (0, 0)

(no "Exon" information available for 1OMO)

(-) 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:320
 aligned with ALADH_ARCFU | O28608 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:320
                                    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
          ALADH_ARCFU     1 METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLMGYAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSLRTGAAGGIAAKYLARKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTTPSRKPVVKAEWVEEGTHINAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGSKIKFF 320
               SCOP domains d1omoa_ A: Archaeal alanine dehydrogenase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhh..hhhhhhhhhhhhhhhhhh........eeee....eeeeeeeee..eeeeeeeee...hhhhh.....eeeeee......eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh...eee.hhhhhh...eeee.........hhhhh....eeee...........hhhhhhheeeee.hhhhhhhhh.hhhhhhh.......eeeehhhhhh...........eeeee...hhhhhhhhhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1omo A   1 METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLMGYAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSLRTGAAGGIAAKYLARKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTTPSRKPVVKAEWVEEGTHINAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGSKIKFF 320
                                    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:320
 aligned with ALADH_ARCFU | O28608 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:320
                                    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
          ALADH_ARCFU     1 METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLMGYAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSLRTGAAGGIAAKYLARKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTTPSRKPVVKAEWVEEGTHINAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGSKIKFF 320
               SCOP domains d1omob_ B: Archaeal alanine dehydrogenase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhh..hhhhhhhhhhhhhhhhhh........eeeee..eeeeeeeeee..eeeeeeeee...hhhhh.....eeeeee......eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh..eeee.hhhhhh...eeee..................eeee...........hhhhhhheeeee.hhhhhhhhh.hhhhhhh...hhhhh.eehhhhhh...........eeeee...hhhhhhhhhhhhhhhhhhhh..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1omo B   1 METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLMGYAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSLRTGAAGGIAAKYLARKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAKKFVSYCEDRGISASVQPAEEASRCDVLVTTTPSRKPVVKAEWVEEGTHINAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGVEDVHATIGEVIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGSKIKFF 320
                                    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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OMO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OMO)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALADH_ARCFU | O28608)
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:0000286    alanine dehydrogenase activity    Catalysis of the reaction: L-alanine + H2O + NAD+ = pyruvate + NH3 + NADH + 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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006522    alanine metabolic process    The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.
    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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 Related Entries

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        ALADH_ARCFU | O28608: 1vll

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