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(-) Description

Title :  CRYSTAL STRUCTURE OF LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH L-MALATE ION
 
Authors :  N. Watanabe, M. M. Cherney, M. J. Van Belkum, S. L. Marcus, M. D. Flegel, M. K. Deyholos, J. C. Vederas, M. N. G. James
Date :  16 May 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ll-Diaminopimelate Aminotransferase, Ll-Dap-At, Plp, Arabidopsis Thaliana, Lysine Biosynthesis, Thdpa, Ll-Dap, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Watanabe, M. M. Cherney, M. J. Van Belkum, S. L. Marcus, M. D. Flegel M. D. Clay, M. K. Deyholos, J. C. Vederas, M. N. James
Crystal Structure Of Ll-Diaminopimelate Aminotransferase From Arabidopsis Thaliana: A Recently Discovered Enzyme In The Biosynthesis Of L-Lysine By Plants And Chlamydia
J. Mol. Biol. V. 371 685 2007
PubMed-ID: 17583737  |  Reference-DOI: 10.1016/J.JMB.2007.05.061

(-) Compounds

Molecule 1 - LL-DIAMINOPIMELATE AMINOTRANSFERASE
    ChainsA, B
    EC Number2.6.1.83
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE60
    Expression System StrainM15(PREP4)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAT4G33680
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymHYPOTHETICAL PROTEIN AT4G33680, HYPOTHETICAL PROTEIN T16L1.170

 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
1MLT1Ligand/IonMALATE ION
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:39 , ILE A:63 , GLY A:64 , TYR A:152 , ASN A:209 , ARG A:404 , PLP A:500 , HOH A:603 , TYR B:94 , ASN B:309BINDING SITE FOR RESIDUE MLT A 433
2AC2SOFTWAREGLY A:127 , ALA A:128 , LYS A:129 , CYS A:205 , ASN A:209 , ASP A:237 , TYR A:240 , SER A:267 , SER A:269 , LYS A:270 , ARG A:278 , MLT A:433 , TYR B:94 , ASN B:309BINDING SITE FOR RESIDUE PLP A 500
3AC3SOFTWARETYR A:94 , ASN A:309 , GLY B:127 , ALA B:128 , LYS B:129 , TYR B:152 , ASN B:209 , ASP B:237 , TYR B:240 , SER B:267 , SER B:269 , LYS B:270 , ARG B:278BINDING SITE FOR RESIDUE PLP B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z1Z)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asp A:149 -Pro A:150
2Ser A:206 -Pro A:207
3Asn A:209 -Pro A:210
4Ala B:35 -Gly B:36
5Asp B:149 -Pro B:150
6Ser B:206 -Pro B:207
7Asn B:209 -Pro B:210
8Glu B:400 -Gly B:401

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z1Z)

(-) 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:408
 aligned with DAPAT_ARATH | Q93ZN9 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:408
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453        
          DAPAT_ARATH    54 EYKTKVSRNSNMSKLQAGYLFPEIARRRSAHLLKYPDAQVISLGIGDTTEPIPEVITSAMAKKAHELSTIEGYSGYGAEQGAKPLRAAIAKTFYGGLGIGDDDVFVSDGAKCDISRLQVMFGSNVTIAVQDPSYPAYVDSSVIMGQTGQFNTDVQKYGNIEYMRCTPENGFFPDLSTVGRTDIIFFCSPNNPTGAAATREQLTQLVEFAKKNGSIIVYDSAYAMYMSDDNPRSIFEIPGAEEVAMETASFSKYAGFTGVRLGWTVIPKKLLYSDGFPVAKDFNRIICTCFNGASNISQAGALACLTPEGLEAMHKVIGFYKENTNIIIDTFTSLGYDVYGGKNAPYVWVHFPNQSSWDVFAEILEKTHVVTTPGSGFGPGGEGFVRVSAFGHRENILEACRRFKQLYK 461
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhh...hhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh....ee....ee..eeeee.hhhhh............eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh......hhhhh.hhhh.eeeeeehhhhhh......eeee...........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z1z A  19 EYKTKVSRNSNMSKLQAGYLFPEIARRRSAHLLKYPDAQVISLGIGDTTEPIPEVITSAMAKKAHELSTIEGYSGYGAEQGAKPLRAAIAKTFYGGLGIGDDDVFVSDGAKCDISRLQVMFGSNVTIAVQDPSYPAYVDSSVIMGQTGQFNTDVQKYGNIEYMRCTPENGFFPDLSTVGRTDIIFFCSPNNPTGAAATREQLTQLVEFAKKNGSIIVYDSAYAMYMSDDNPRSIFEIPGAEEVAMETASFSKYAGFTGVRLGWTVIPKKLLYSDGFPVAKDFNRIICTCFNGASNISQAGALACLTPEGLEAMHKVIGFYKENTNIIIDTFTSLGYDVYGGKNAPYVWVHFPNQSSWDVFAEILEKTHVVTTPGSGFGPGGEGFVRVSAFGHRENILEACRRFKQLYK 426
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418        

Chain B from PDB  Type:PROTEIN  Length:408
 aligned with DAPAT_ARATH | Q93ZN9 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:408
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453        
          DAPAT_ARATH    54 EYKTKVSRNSNMSKLQAGYLFPEIARRRSAHLLKYPDAQVISLGIGDTTEPIPEVITSAMAKKAHELSTIEGYSGYGAEQGAKPLRAAIAKTFYGGLGIGDDDVFVSDGAKCDISRLQVMFGSNVTIAVQDPSYPAYVDSSVIMGQTGQFNTDVQKYGNIEYMRCTPENGFFPDLSTVGRTDIIFFCSPNNPTGAAATREQLTQLVEFAKKNGSIIVYDSAYAMYMSDDNPRSIFEIPGAEEVAMETASFSKYAGFTGVRLGWTVIPKKLLYSDGFPVAKDFNRIICTCFNGASNISQAGALACLTPEGLEAMHKVIGFYKENTNIIIDTFTSLGYDVYGGKNAPYVWVHFPNQSSWDVFAEILEKTHVVTTPGSGFGPGGEGFVRVSAFGHRENILEACRRFKQLYK 461
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------Aminotran_1_2-2z1zB01 B:56-421                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------Aminotran_1_2-2z1zB02 B:56-421                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains (2)
         Sec.struct. author ........hhhhhhh...hhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh....ee....ee...eeee.hhhhh...hhhhh....eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh......hhhhh.hhhh.eeeeee............eeee...........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eeeee....hhhhhhhhhhhhhhee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z1z B  19 EYKTKVSRNSNMSKLQAGYLFPEIARRRSAHLLKYPDAQVISLGIGDTTEPIPEVITSAMAKKAHELSTIEGYSGYGAEQGAKPLRAAIAKTFYGGLGIGDDDVFVSDGAKCDISRLQVMFGSNVTIAVQDPSYPAYVDSSVIMGQTGQFNTDVQKYGNIEYMRCTPENGFFPDLSTVGRTDIIFFCSPNNPTGAAATREQLTQLVEFAKKNGSIIVYDSAYAMYMSDDNPRSIFEIPGAEEVAMETASFSKYAGFTGVRLGWTVIPKKLLYSDGFPVAKDFNRIICTCFNGASNISQAGALACLTPEGLEAMHKVIGFYKENTNIIIDTFTSLGYDVYGGKNAPYVWVHFPNQSSWDVFAEILEKTHVVTTPGSGFGPGGEGFVRVSAFGHRENILEACRRFKQLYK 426
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418        

   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 2Z1Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z1Z)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DAPAT_ARATH | Q93ZN9)
molecular function
    GO:0010285    L,L-diaminopimelate aminotransferase activity    Catalysis of the reaction: 2-oxoglutarate + LL-2,6-diaminopimelate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H(2)O + H(+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    GO:0009735    response to cytokinin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokinin stimulus.
    GO:0009862    systemic acquired resistance, salicylic acid mediated signaling pathway    The series of molecular signals mediated by salicylic acid involved in systemic acquired resistance.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPAT_ARATH | Q93ZN92z20 3ei5 3ei6 3ei7 3ei8 3ei9 3eia 3eib

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z1Z)