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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF TETRAHYDRODIPICOLINATE-N-SUCCINLYTRANSFERASE
 
Authors :  T. W. Beaman, D. W. Binder, J. S. Blanchard, S. L. Roderick
Date :  19 Nov 96  (Deposition) - 05 Jun 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Succinyltransferase, Lysine Metabolism, Hexapeptide Transferase, Cell Wall Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. W. Beaman, D. A. Binder, J. S. Blanchard, S. L. Roderick
Three-Dimensional Structure Of Tetrahydrodipicolinate N-Succinyltransferase.
Biochemistry V. 36 489 1997
PubMed-ID: 9012664  |  Reference-DOI: 10.1021/BI962522Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETRAHYDRODIPICOLINATE-N-SUCCINLYTRANSFERASE
    Cell Line: BL21
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Organism Scientific: MYCOBACTERIUM BOVIS
    Organism Taxid: 1765
    Synonym: THDP-SUCCINYLTRANSFERASE, DAPD

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1TDT)

(-) Sites  (0, 0)

(no "Site" information available for 1TDT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:107 -Pro A:108
2Glu A:169 -Pro A:170
3Pro B:107 -Pro B:108
4Glu B:169 -Pro B:170
5Pro C:107 -Pro C:108
6Glu C:169 -Pro C:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TDT)

(-) 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:256
 aligned with DAPD_UNKP | P56220 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:256
                                    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      
            DAPD_UNKP     1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKV 256
               SCOP domains d1tdta_ A: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD                                                                                                                                                                          SCOP domains
               CATH domains 1tdtA01 A:1-70                                                        ----------------1tdtA02 A:87-256 Hexapeptide repeat proteins                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh......eeee..eeee.hhhhhhhhhhhhh...eeee....eeee..........hhhhhhh........................eee...............eee...................................................................eee....eee.......eeeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tdt A   1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKV 256
                                    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      


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with DAPD_UNKP | P56220 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
            DAPD_UNKP     2 QQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKV 256
               SCOP domains d1tdtb_ B: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD                                                                                                                                                                         SCOP domains
               CATH domains 1tdtB01 B:2-70                                                       ----------------1tdtB02 B:87-256 Hexapeptide repeat proteins                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....eeee..eeee.hhhhhhhhhhhhh...eeee....eeee..........hhhhhhh........................eee...............eee...................................................................eee..............eeeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tdt B   2 QQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKV 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     


Chain C from PDB  Type:PROTEIN  Length:253
 aligned with DAPD_UNKP | P56220 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
            DAPD_UNKP     4 LQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKV 256
               SCOP domains d1tdtc_ C: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD                                                                                                                                                                       SCOP domains
               CATH domains 1tdtC01 C:4-70                                                     ----------------1tdtC02 C:87-256 Hexapeptide repeat proteins                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh......eeee..eeee.hhhhhhhhhhhhh...eeee....eeee..........hhhhhhh........................eee...............eee...................................................................eee................eeeeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tdt C   4 LQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKV 256
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
   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, 3)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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

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

UniProtKB/Swiss-Prot
        DAPD_UNKP | P56220: 1kgq 1kgt 2tdt 3tdt

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