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(-) Description

Title :  L,L-DIAMINOPIMELATE AMINOTRANSFERASE FROM CHALMYDOMONAS REINHARDTII
 
Authors :  R. C. J. Dobson, I. Giron, A. O. Hudson
Date :  25 Jan 11  (Deposition) - 01 Jun 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-Lysine, L, L-Diaminopimelate Aminotransferase, Pyridoxal-5'- Phosphate, Chamydomonas Reinhardtii, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. J. Dobson, I. Giron, A. O. Hudson
L, L-Diaminopimelate Aminotransferase From Chlamydomonas Reinhardtii: A Target For Algaecide Development
Plos One V. 6 E2043 2011
PubMed-ID: 21633707  |  Reference-DOI: 10.1371/JOURNAL.PONE.0020439

(-) Compounds

Molecule 1 - LL-DIAMINOPIMELATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.83
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DPA1
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1AZI3Ligand/IonAZIDE ION
2GOL2Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:282 , GLY A:288 , ARG A:290 , ARG B:101 , GLY B:103 , TYR B:104 , ASN B:325 , HOH B:477BINDING SITE FOR RESIDUE SO4 A 450
2AC2SOFTWAREGLY A:140 , SER A:141 , LYS A:142 , SER A:279 , SER A:281 , TYR A:283 , HOH A:473 , HOH A:594 , ASN B:321BINDING SITE FOR RESIDUE SO4 A 451
3AC3SOFTWAREPHE A:124 , ALA A:249 , ALA A:250 , ALA A:252 , LEU A:253 , CYS A:278 , SER A:279 , PHE A:280 , TRP A:293 , HOH A:493 , HOH A:640BINDING SITE FOR RESIDUE GOL A 452
4AC4SOFTWARETHR A:34 , ASP A:36 , HIS B:127 , ARG B:239 , LYS B:240 , GLY B:242BINDING SITE FOR RESIDUE AZI A 453
5AC5SOFTWAREGLU A:81 , MET A:346 , PHE A:349 , HOH A:576 , HOH A:587 , HOH A:642BINDING SITE FOR RESIDUE AZI A 454
6AC6SOFTWAREARG A:101 , GLY A:103 , TYR A:104 , ASN A:325 , LYS B:282 , GLY B:288 , ARG B:290 , HOH B:487BINDING SITE FOR RESIDUE SO4 B 450
7AC7SOFTWAREASN A:321 , GLY B:140 , SER B:141 , LYS B:142 , SER B:279 , SER B:281 , TYR B:283 , HOH B:461 , HOH B:584BINDING SITE FOR RESIDUE SO4 B 451
8AC8SOFTWAREALA B:249 , ALA B:250 , ALA B:252 , LEU B:253 , CYS B:278 , SER B:279 , PHE B:280 , HOH B:632 , HOH B:688BINDING SITE FOR RESIDUE GOL B 452

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:108 -Ala A:109
2Asp A:162 -Pro A:163
3Ser A:217 -Pro A:218
4Asn A:220 -Pro A:221
5Gly B:108 -Ala B:109
6Asp B:162 -Pro B:163
7Ser B:217 -Pro B:218
8Asn B:220 -Pro B:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QGU)

(-) Exons   (0, 0)

(no "Exon" information available for 3QGU)

(-) 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:406
 aligned with A8IW39_CHLRE | A8IW39 from UniProtKB/TrEMBL  Length:441

    Alignment length:406
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432      
         A8IW39_CHLRE    33 GTIDVQRNENFGKLRAGYLFPEIARRRKAHQEKNPDAKIISLGIGDTTEPLPKYIADAMAKAAAGLATREGYSGYGAEQGQGALREAVASTFYGHAGRAADEIFISDGSKCDIARIQMMFGSKPTVAVQDPSYPVYVDTSVMMGMTGDHNGTGFDGIEYMVCNPDNHFFPDLSKAKRTDIIFFCSPNNPTGAAATRAQLTELVNFARKNGSILVYDAAYALYISNPDCPKTIYEIPGADEVAIETCSFSKYAGFTGVRLGWTVVPKALKYANGEPVHADWNRVMTTCFNGASNIVQAGGLACLQPEGLKEMNAMIKFYKENAQILKTTFTEMGFSVYGGDDAPYIWVGFPGKPSWDVFAEILERCNIVTTPGSGFGPAGEGFVRASAFGSRENILEAVRRFKEAYG 438
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh...hhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh............eeeee.hhhhh...hhhhh....eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh.......hhhhh.hhhh.eeeeee.hhhhh......eeee...........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qgu A  33 GTIDVQRNENFGKLRAGYLFPEIARRRKAHQEKNPDAKIISLGIGDTTEPLPKYIADAMAKAAAGLATREGYSGYGAEQGQGALREAVASTFYGHAGRAADEIFISDGSKCDIARIQMMFGSKPTVAVQDPSYPVYVDTSVMMGMTGDHNGTGFDGIEYMVCNPDNHFFPDLSKAKRTDIIFFCSPNNPTGAAATRAQLTELVNFARKNGSILVYDAAYALYISNPDCPKTIYEIPGADEVAIETCSFSKYAGFTGVRLGWTVVPKALKYANGEPVHADWNRVMTTCFNGASNIVQAGGLACLQPEGLKEMNAMIKFYKENAQILKTTFTEMGFSVYGGDDAPYIWVGFPGKPSWDVFAEILERCNIVTTPGSGYGPAGEGFVRASAFGSRENILEAVRRFKEAYG 438
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432      


Chain B from PDB  Type:PROTEIN  Length:413
 aligned with A8IW39_CHLRE | A8IW39 from UniProtKB/TrEMBL  Length:441

    Alignment length:413
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435   
         A8IW39_CHLRE    26 QAVAQRAGTIDVQRNENFGKLRAGYLFPEIARRRKAHQEKNPDAKIISLGIGDTTEPLPKYIADAMAKAAAGLATREGYSGYGAEQGQGALREAVASTFYGHAGRAADEIFISDGSKCDIARIQMMFGSKPTVAVQDPSYPVYVDTSVMMGMTGDHNGTGFDGIEYMVCNPDNHFFPDLSKAKRTDIIFFCSPNNPTGAAATRAQLTELVNFARKNGSILVYDAAYALYISNPDCPKTIYEIPGADEVAIETCSFSKYAGFTGVRLGWTVVPKALKYANGEPVHADWNRVMTTCFNGASNIVQAGGLACLQPEGLKEMNAMIKFYKENAQILKTTFTEMGFSVYGGDDAPYIWVGFPGKPSWDVFAEILERCNIVTTPGSGFGPAGEGFVRASAFGSRENILEAVRRFKEAYG 438
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------Aminotran_1_2-3qguB01 B:69-433                                                                                                                                                                                                                                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------------Aminotran_1_2-3qguB02 B:69-433                                                                                                                                                                                                                                                                                                                                               ----- Pfam domains (2)
         Sec.struct. author hhhhhh........hhhhhhh...hhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhh.............eeeee.hhhhh............eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh.......hhhhh.hhhh.eeeeee.hhhhh......eeee...........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qgu B  26 QAVAQRAGTIDVQRNENFGKLRAGYLFPEIARRRKAHQEKNPDAKIISLGIGDTTEPLPKYIADAMAKAAAGLATREGYSGYGAEQGQGALREAVASTFYGHAGRAADEIFISDGSKCDIARIQMMFGSKPTVAVQDPSYPVYVDTSVMMGMTGDHNGTGFDGIEYMVCNPDNHFFPDLSKAKRTDIIFFCSPNNPTGAAATRAQLTELVNFARKNGSILVYDAAYALYISNPDCPKTIYEIPGADEVAIETCSFSKYAGFTGVRLGWTVVPKALKYANGEPVHADWNRVMTTCFNGASNIVQAGGLACLQPEGLKEMNAMIKFYKENAQILKTTFTEMGFSVYGGDDAPYIWVGFPGKPSWDVFAEILERCNIVTTPGSGYGPAGEGFVRASAFGSRENILEAVRRFKEAYG 438
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435
   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 3QGU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A8IW39_CHLRE | A8IW39)
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.

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