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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE FROM E. COLI
 
Authors :  G. Kozlov, K. Gehring, Montreal-Kingston Bacterial Structural Ge Initiative (Bsgi)
Date :  15 Jan 08  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Left-Handed Beta-Helix, Structural Genomics, Cihr, Canadian Institutes Of Health Research, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Acyltransferase, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lysine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Nguyen, G. Kozlov, K. Gehring
Structure Of Escherichia Coli Tetrahydrodipicolinate N-Succinyltransferase Reveals The Role Of A Conserved C-Terminal Helix In Cooperative Substrate Binding.
Febs Lett. V. 582 623 2008
PubMed-ID: 18242192  |  Reference-DOI: 10.1016/J.FEBSLET.2008.01.032

(-) Compounds

Molecule 1 - 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- SUCCINYLTRANSFERASE
    Chains: A
    EC Number: 2.3.1.117
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PFO4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83334
    Synonym: TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE, THP SUCCINYLTRANSFERASE, TETRAHYDROPICOLINATE SUCCINYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:107 -Pro A:108
2Glu A:169 -Pro A:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.DAPD_ECO57134-162  1A:134-162
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.DAPD_ECO57134-162  3A:134-162

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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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:275
 aligned with DAPD_ECO57 | Q8X8Y7 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:278
                                1                                                                                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266        
           DAPD_ECO57     - ----MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGDIHYGRVPAGSVVVSGNLPSKDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
               SCOP domains d3bxya_ A: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD                                                                                                                                                                                                SCOP domains
               CATH domains 3bxyA01 A:-3-70                                                           ----------------3bxyA02 A:87-256 Hexapeptide repeat proteins                                                                                                                              ------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhhh..eeee....eeee.........hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee.hhhhh---hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxy A  -3 HHHGSQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGDIHYGRVPAGSVVVSGNLPSKDGKYSLYCAVIVKKVDAKTR---GINELLRTID 274
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256    |  266        
                                                                                                                                                                                                                                                                                                  261 265
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DAPD_ECO57 | Q8X8Y7)
molecular function
    GO:0008666    2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity    Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H(2)O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA.
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(-) Related Entries Specified in the PDB File

1kgq
1kgt RELATED ID: DAPD_ECO57 RELATED DB: TARGETDB
1tdt
2tdt
3tdt