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(-) Description

Title :  COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINOPIMELATE AND COENZYME A
 
Authors :  T. W. Beaman, J. S. Blanchard, S. L. Roderick
Date :  05 May 98  (Deposition) - 14 Oct 98  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Acyltransferase, Lysine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Beaman, J. S. Blanchard, S. L. Roderick
The Conformational Change And Active Site Structure Of Tetrahydrodipicolinate N-Succinyltransferase.
Biochemistry V. 37 10363 1998
PubMed-ID: 9671504  |  Reference-DOI: 10.1021/BI980759B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE
    Cell Line: BL21
    Chains: A
    EC Number: 2.3.1.117
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: DAPD
    Expression System Plasmid: PET3A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DAPD
    Organism Scientific: MYCOBACTERIUM BOVIS
    Organism Taxid: 1765
    Synonym: DAPD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2NPI1Ligand/Ion(2S)-2-AMINOHEPTANEDIOIC ACID
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1COA3Ligand/IonCOENZYME A
2NPI3Ligand/Ion(2S)-2-AMINOHEPTANEDIOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:141 , SER A:159 , GLY A:160 , GLY A:185 , ALA A:186 , GLU A:192 , SER A:203 , MET A:204 , SER A:211 , ARG A:213 , ARG A:217 , TYR A:248 , VAL A:253 , LYS A:254 , LYS A:259 , THR A:260 , LYS A:263 , HOH A:334 , HOH A:338 , HOH A:350 , HOH A:352 , HOH A:383BINDING SITE FOR RESIDUE COA A 280
2AC2SOFTWAREPHE A:67 , ARG A:104 , ARG A:112 , ASN A:129 , MET A:139 , ASP A:141 , SER A:148 , GLY A:166 , VAL A:167 , LEU A:168 , GLU A:169 , HOH A:325 , HOH A:383BINDING SITE FOR RESIDUE NPI A 281

(-) SS Bonds  (0, 0)

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

(-) 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 2TDT)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.DAPD_UNKP134-162  1A:134-162
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.DAPD_UNKP134-162  3A:134-162

(-) Exons   (0, 0)

(no "Exon" information available for 2TDT)

(-) 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:274
 aligned with DAPD_UNKP | P56220 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:274
                                    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    
            DAPD_UNKP     1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
               SCOP domains d2tdta_ A: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD                                                                                                                                                                                            SCOP domains
               CATH domains 2tdtA01 A:1-70                                                        ----------------2tdtA02 A:87-256 Hexapeptide repeat proteins                                                                                                                              ------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....eeee..eeee.hhhhhhhhhhhhh...eeee....eeee....hhh...hhhhhhh........................eee...............eee...................................................................eee..............eeeeeeeee......eeeeeeeeee..hhhhhhh...hhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tdt A   1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
                                    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
   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, 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 2TDT)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DAPD_UNKP | P56220)
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

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        DAPD_UNKP | P56220: 1kgq 1kgt 1tdt 3tdt

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