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(-) Description

Title :  C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE
 
Authors :  G. Scapin, M. Cirilli, S. G. Reddy, Y. Gao, J. C. Vederas, J. S. Blanchard
Date :  29 Dec 97  (Deposition) - 08 Apr 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Nadp, Dehydrogenase, D-Amino Acid Dehydrogenase, Lysine Biosynthesis, Asymmetric Dimer, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Scapin, M. Cirilli, S. G. Reddy, Y. Gao, J. C. Vederas, J. S. Blanchard
Substrate And Inhibitor Binding Sites In Corynebacterium Glutamicum Diaminopimelate Dehydrogenase.
Biochemistry V. 37 3278 1998
PubMed-ID: 9521647  |  Reference-DOI: 10.1021/BI9727949
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIAMINOPIMELIC ACID DEHYDROGENASE
    Cell Line: BL21
    Chains: A, B
    EC Number: 1.4.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: DAPDH
    Expression System Plasmid: PET23A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: DAPDH
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: DAPDH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1DA31Ligand/Ion(2S,5',S)-2-AMINO-3-(3-CARBOXY-2-ISOXAZOLIN-5-YL)PROPANOIC ACID
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , TYR A:11 , GLY A:12 , ASN A:13 , LEU A:14 , SER A:35 , ARG A:36 , ARG A:37 , CYS A:65 , MET A:66 , GLY A:67 , SER A:68 , THR A:88 , ASP A:90 , THR A:117 , GLY A:118 , TRP A:119 , ASP A:120 , PRO A:121 , ASN A:270 , THR A:274 , HOH A:1001 , HOH A:1002 , HOH A:1021BINDING SITE FOR RESIDUE NDP A 401
2AC2SOFTWAREGLY B:10 , TYR B:11 , GLY B:12 , ASN B:13 , LEU B:14 , SER B:35 , ARG B:36 , ARG B:37 , CYS B:65 , MET B:66 , GLY B:67 , SER B:68 , THR B:88 , ASP B:90 , THR B:117 , GLY B:118 , TRP B:119 , ASP B:120 , PRO B:121 , GLN B:150 , GLY B:151 , ARG B:157 , ASN B:270 , THR B:274 , DA3 B:950 , HOH B:1055 , HOH B:1056 , HOH B:1057 , HOH B:1058 , HOH B:1059 , HOH B:1061BINDING SITE FOR RESIDUE NDP B 901
3AC3SOFTWAREASP B:90 , TRP B:119 , ASP B:120 , TRP B:144 , SER B:149 , GLN B:150 , GLY B:151 , THR B:169 , ARG B:195 , HIS B:244 , ASN B:270 , NDP B:901BINDING SITE FOR RESIDUE DA3 B 950
4INHUNKNOWNASP B:90 , HIS B:92 , ASP B:120 , GLN B:150 , GLY B:151 , THR B:169 , ARG B:195 , HIS B:244 , ASN B:270INHIBITOR BINDING SITE IN SECOND MOLECULE.
5N1UNKNOWNGLY A:10 , TYR A:11 , GLY A:12 , ASN A:13 , GLY A:15 , SER A:35 , ARG A:36 , ARG A:37 , CYS A:65 , SER A:68 , ASP A:90 , THR A:117 , GLY A:118 , TRP A:119 , ASP A:120NADP+ BINDING SITE IN FIRST MOLECULE.
6N2UNKNOWNGLY B:10 , TYR B:11 , GLY B:12 , ASN B:13 , LEU B:14 , GLY B:15 , SER B:35 , ARG B:36 , ARG B:37 , CYS B:65 , SER B:68 , ASP B:90 , THR B:117 , GLY B:118 , TRP B:119 , ASP B:120 , GLN B:150 , ARG B:157NADP+ BINDING SITE IN SECOND MOLECULE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:145 -Pro A:146
2Asp B:120 -Pro B:121
3Gly B:145 -Pro B:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DAP)

(-) 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 DAPDH_CORGL | P04964 from UniProtKB/Swiss-Prot  Length:320

    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
          DAPDH_CORGL     1 MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV 320
               SCOP domains d3dapa1 A:1-118,A:269-320 Diaminopimelic acid dehydrogenase (DAPDH)                                                   d3dapa2 A:119-268 Diaminopimelic acid dehydrogenase (DAPDH)                                                                                           d3dapa1 A:1-118,A:269-320                            SCOP domains
               CATH domains 3dapA01 A:1-123,A:267-311 NAD(P)-binding Rossmann-like Domain                                                              ---3dapA02 A:127-264 Dihydrodipicolinate Reductase; domain 2                                                                                 --3dapA01 A:1-123,A:267-311                    --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhh...eeeeeeee..........eeehhhhhhhhhh..eeee......hhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh....eeeeee.....hhhhhhhhh.....eeeeeeee.hhhhhhhhh.......hhhheeeeeeee..hhhhhhhhhhhh..........eeeee..hhhhhhh.....eeeeeeeeee....eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh....eeeehhh..hhhh....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dap A   1 MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV 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 DAPDH_CORGL | P04964 from UniProtKB/Swiss-Prot  Length:320

    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
          DAPDH_CORGL     1 MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV 320
               SCOP domains d3dapb1 B:1-118,B:269-320 Diaminopimelic acid dehydrogenase (DAPDH)                                                   d3dapb2 B:119-268 Diaminopimelic acid dehydrogenase (DAPDH)                                                                                           d3dapb1 B:1-118,B:269-320                            SCOP domains
               CATH domains 3dapB01 B:1-123,B:267-311 NAD(P)-binding Rossmann-like Domain                                                              ---3dapB02 B:127-264 Dihydrodipicolinate Reductase; domain 2                                                                                 --3dapB01 B:1-123,B:267-311                    --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhh....eeeeeeee..........eeehhhhhhhhhh..eeee......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhh...eeeeeee.....hhhhhhhhh.....eeeeeeee.hhhhhhhhh.......hhhheeeeeeee..hhhhhhhhhhhh.........eeeeee..hhhhhhh.....eeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh....eee.hhh..hhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dap B   1 MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV 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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DAPDH_CORGL | P04964)
molecular function
    GO:0047850    diaminopimelate dehydrogenase activity    Catalysis of the reaction: meso-2,6-diaminopimelate + H(2)O + NADP(+) = L-2-amino-6-oxopimelate + H(+) + NADPH + NH(4)(+).
    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: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: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: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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DAPDH_CORGL | P04964: 1dap 1f06 2dap

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