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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE
 
Authors :  M. Cirilli, G. Scapin, A. Sutherland, J. F. Caplan, J. C. Vederas, J. S. B
Date :  14 May 00  (Deposition) - 14 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Enzyme-Nadph-Inhibitor Ternary Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Cirilli, G. Scapin, A. Sutherland, J. C. Vederas, J. S. Blanchard
The Three-Dimensional Structure Of The Ternary Complex Of Corynebacterium Glutamicum Diaminopimelate Dehydrogenase-Nadph-L-2-Amino-6-Methylene-Pimelate.
Protein Sci. V. 9 2034 2000
PubMed-ID: 11106178

(-) Compounds

Molecule 1 - MESO-DIAMINOPIMELATE D-DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
12NP1Ligand/IonL-2-AMINO-6-METHYLENE-PIMELIC ACID
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12NP-1Ligand/IonL-2-AMINO-6-METHYLENE-PIMELIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12NP1Ligand/IonL-2-AMINO-6-METHYLENE-PIMELIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
12NP1Ligand/IonL-2-AMINO-6-METHYLENE-PIMELIC ACID
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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 , TRP A:119 , ASP A:120 , PRO A:121 , ASN A:270 , THR A:274 , HOH A:1008 , HOH A:1056 , HOH A:1112BINDING SITE FOR RESIDUE NDP A 401
2AC2SOFTWAREGLY B:510 , TYR B:511 , GLY B:512 , ASN B:513 , LEU B:514 , SER B:535 , ARG B:536 , ARG B:537 , CYS B:565 , MET B:566 , GLY B:567 , SER B:568 , THR B:588 , ASP B:590 , THR B:617 , GLY B:618 , TRP B:619 , ASP B:620 , PRO B:621 , GLN B:650 , GLY B:651 , ASP B:654 , ARG B:657 , ASN B:770 , THR B:774 , 2NP B:950 , HOH B:1002 , HOH B:1018 , HOH B:1029 , HOH B:1134 , HOH B:1147BINDING SITE FOR RESIDUE NDP B 901
3AC3SOFTWAREASP B:590 , TRP B:619 , ASP B:620 , TRP B:644 , SER B:649 , GLN B:650 , GLY B:651 , HIS B:652 , THR B:669 , ARG B:695 , HIS B:744 , ASN B:770 , NDP B:901BINDING SITE FOR RESIDUE 2NP B 950

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F06)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:120 -Pro A:121
2Gly A:145 -Pro A:146
3Asp B:620 -Pro B:621
4Gly B:645 -Pro B:646

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F06)

(-) Exons   (0, 0)

(no "Exon" information available for 1F06)

(-) 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: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 d1f06a1 A:1-118,A:269-320 Diaminopimelic acid dehydrogenase (DAPDH)                                                   d1f06a2 A:119-268 Diaminopimelic acid dehydrogenase (DAPDH)                                                                                           d1f06a1 A:1-118,A:269-320                            SCOP domains
               CATH domains 1f06A01 A:1-123,A:267-311 NAD(P)-binding Rossmann-like Domain                                                              ---1f06A02 A:127-264 Dihydrodipicolinate Reductase; domain 2                                                                                 --1f06A01 A:1-123,A:267-311                    --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhh....eeeeeeee..........eee.hhhhhh.....eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eehhhhhhhhhh.....eeeeeeeehhhhhhhhhhh.....hhhhheeeeeeee.hhhhhhhhhhhhhh........eeeeee.hhhhhhhhh....eeeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f06 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 d1f06b1 B:501-618,B:769-820 Diaminopimelic acid dehydrogenase (DAPDH)                                                 d1f06b2 B:619-768 Diaminopimelic acid dehydrogenase (DAPDH)                                                                                           d1f06b1 B:501-618,B:769-820                          SCOP domains
               CATH domains 1f06B01 B:501-623,B:767-811 NAD(P)-binding Rossmann-like Domain                                                            ---1f06B02 B:627-764 Dihydrodipicolinate Reductase; domain 2                                                                                 --1f06B01 B:501-623,B:767-811                  --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhh....eeeeeeee..........eee.hhhhhh.....eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eehhhhhhhhhh...eeeeeeeeeehhhhhhhhhh...........eeeeeeeee...hhhhhhhhhhh........eeeeee.hhhhhhhhh....eeeeeeeeee....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f06 B 501 MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV 820
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F06)

(-) Gene Ontology  (7, 7)

Asymmetric 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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  1f06
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  DAPDH_CORGL | P04964
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  1.4.1.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPDH_CORGL | P04964: 1dap 2dap 3dap

(-) Related Entries Specified in the PDB File

1dap 1DAP CONTAINS NATIVE DIAMINOPIMELIC ACID DEHYDROGENASE
2dap 2DAP CONTAINS THREE-DIMENSIONAL STRUCTURE OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE AS A BINARY COMPLEX WITH THE SUBSTRATE MESO-DIAMINOPIMELATE (MESO-DAP)
3dap 3DAP CONTAINS THE THREE-DIMENSIONAL STRUCTURES OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE AS A TERNARY COMPLEX WITH WITH NADP+ AND AN ISOXAZOLINE INHIBITOR