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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-LL-DIAMINOPIMELATE AMINOTRANSFERASE FROM CHLAMYDIA TRACHOMATIS
 
Authors :  N. Watanabe, M. N. James
Date :  10 Dec 10  (Deposition) - 31 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plp Dependent Aminotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Watanabe, M. D. Clay, M. J. Van Belkum, C. Fan, J. C. Vederas, M. N. James
The Structure Of Ll-Diaminopimelate Aminotransferase From Chlamydia Trachomatis: Implications For Its Broad Substrate Specificity.
J. Mol. Biol. V. 411 649 2011
PubMed-ID: 21722650  |  Reference-DOI: 10.1016/J.JMB.2011.06.023

(-) Compounds

Molecule 1 - LL-DIAMINOPIMELATE AMINOTRANSFERASE
    ChainsA
    EC Number2.6.1.83
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDAPL, ASPC, CT_390
    Organism ScientificCHLAMYDIA TRACHOMATIS
    Organism Taxid813
    SynonymDAP-AT, DAP-AMINOTRANSFERASE, LL-DAP-AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ASA)

(-) Sites  (0, 0)

(no "Site" information available for 3ASA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ASA)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Asn A:13 -Tyr A:14
2Thr A:66 -Thr A:67
3Thr A:67 -Cys A:68
4Arg A:69 -Gly A:70
5Gly A:72 -Pro A:73
6Asp A:125 -Pro A:126
7Ser A:171 -Pro A:172
8Asn A:174 -Pro A:175
9Thr A:333 -Gln A:334

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.DAPAT_CHLTR233-246  1A:233-246
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.DAPAT_CHLTR233-246  2A:233-246

(-) Exons   (0, 0)

(no "Exon" information available for 3ASA)

(-) 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:388
 aligned with DAPAT_CHLTR | O84395 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:388
                                    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       330       340       350       360       370       380        
          DAPAT_CHLTR     1 MKRNPHFVSLTKNYLFADLQKRVAQFRLENPQHTVINLSIGDTTQPLNASVAEAFASSIARLSSPTTCRGYGPDFGLPALRQKLSEDFYRGFVDAKEIFISDGAKVDLFRLLSFFGPNQTVAIQDPSYPAYLDIARLTGAKEIIALPCLQENAFFPEFPEDTHIDILCLCSPNNPTGTVLNKDQLRAIVHYAIEHEILILFDAAYSTFISDPSLPKSIFEIPDARFCAIEINSFSKPLGFAGIRLGWTVIPQELTYADGHFVIQDWERFLSTTFNGASIPAQEAGVAGLSILPQLEAIHYYRENSDLLRKALLATGFEVFGGEHAPYLWVKPTQANISDRDLFDFFLREYHIAITPGIGFGRSGSGFVRFSSLGKREDILAACERLQM 388
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh....hhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhhhh.............hhhhhhhhhhh......hhh.eeee.hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh...eeeeee.hhhhh............eeeee..........hhhhhhhhhhhhhhh..eeeee..hhhhh.......hhhhh.hhhh.eeeeee.hhhhh......eeee...........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee.....eeeee.........hhhhhhhhhhhee.ee.hhhhhhhh..eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asa A   1 MKRNPHFVSLTKNYLFADLQKRVAQFRLENPQHTVINLSIGDTTQPLNASVAEAFASSIARLSSPTTCRGYGPDFGLPALRQKLSEDFYRGFVDAKEIFISDGAKVDLFRLLSFFGPNQTVAIQDPSYPAYLDIARLTGAKEIIALPCLQENAFFPEFPEDTHIDILCLCSPNNPTGTVLNKDQLRAIVHYAIEHEILILFDAAYSTFISDPSLPKSIFEIPDARFCAIEINSFSKPLGFAGIRLGWTVIPQELTYADGHFVIQDWERFLSTTFNGASIPAQEAGVAGLSILPQLEAIHYYRENSDLLRKALLATGFEVFGGEHAPYLWVKPTQANISDRDLFDFFLREYHIAITPGIGFGRSGSGFVRFSSLGKREDILAACERLQM 388
                                    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       330       340       350       360       370       380        

   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 3ASA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ASA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DAPAT_CHLTR | O84395)
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: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:0033362    lysine biosynthetic process via diaminopimelate, diaminopimelate-aminotransferase pathway    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in two enzymatic steps.

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  Cis Peptide Bonds
    Arg A:69 - Gly A:70   [ RasMol ]  
    Asn A:13 - Tyr A:14   [ RasMol ]  
    Asn A:174 - Pro A:175   [ RasMol ]  
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    Gly A:72 - Pro A:73   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPAT_CHLTR | O843953asb

(-) Related Entries Specified in the PDB File

3asb