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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE PSEUDOMONAS DACUNHAE ASPARTATE-BETA-DECARBOXYLASE REVEALS A NOVEL OLIGOMERIC ASSEMBLY FOR A PYRIDOXAL-5-PHOSPHATE DEPENDENT ENZYME
 
Authors :  S. Lima, B. Sundararaju, C. Huang, R. Khristoforov, C. Momany, R. S. Phi
Date :  25 Nov 08  (Deposition) - 17 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  L-Aspartate-Beta-Decarboxylase, Aspartate 4-Decarboxylase, L- Aspartate 4-Carboxy-Lyase, Pyridoxal-5'-Phosphate, Plp, Aspd, Dodecamer, Abdc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lima, B. Sundararaju, C. Huang, R. Khristoforov, C. Momany, R. S. Phillips
The Crystal Structure Of The Pseudomonas Dacunhae Aspartate-Beta-Decarboxylase Dodecamer Reveals An Unknown Oligomeric Assembly For A Pyridoxal-5'-Phosphate-Dependent Enzyme.
J. Mol. Biol. V. 388 98 2009
PubMed-ID: 19265705  |  Reference-DOI: 10.1016/J.JMB.2009.02.055

(-) Compounds

Molecule 1 - L-ASPARTATE-BETA-DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET100
    Organism Scientific: PSEUDOMONAS DACUNHAE ATCC 21192
    Organism Taxid: 207291

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3PLP12Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , TYR A:134 , GLY A:173 , GLY A:174 , THR A:175 , PHE A:204 , TYR A:207 , VAL A:252 , ASN A:256 , ASP A:286 , TYR A:289 , SER A:312 , SER A:314 , LYS A:315 , ARG A:323BINDING SITE FOR RESIDUE PLP A 534
2AC2SOFTWAREASN A:41 , SER A:65 , SER A:67 , GLN A:113 , ASN A:504 , HOH A:584BINDING SITE FOR RESIDUE ACT A 535
3AC3SOFTWAREARG A:49 , ARG A:53 , GLY A:99BINDING SITE FOR RESIDUE CL A 536

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Arg A:37 -Gly A:38
2Val A:136 -Pro A:137
3Met A:201 -Pro A:202
4Asn A:253 -Pro A:254
5Asn A:256 -Pro A:257
6Gly A:428 -Thr A:429
7Arg A:487 -Gly A:488
8Gly A:488 -Phe A:489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FDD)

(-) 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:502
 aligned with Q845W8_COMTE | Q845W8 from UniProtKB/TrEMBL  Length:533

    Alignment length:502
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526  
         Q845W8_COMTE    27 DGNRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAESELSYSYMNTVGVGGLAKIEGIEGRFERYIAENRDQEGVRFLGKSLSYVRDQLGLDPAAFLHEMVDGILGCNYPVPPRMLNISEKIVRQYIIREMGADAIPSESVNLFAVEGGTAAMAYIFESMKVNGLLKAGDKVAIGMPVFTPYIEIPELAQYALEEVAINADPALNWQYPDSELDKLKDPAIKIFFCVNPSNPPSVKMDERSLERVRKIVAEHRPDLMILTDDVYGTFADGFQSLFAICPANTLLVYSFSKYFGATGWRLGVVAAHKENIFDLALGRLPESEKTALDDRYRSLLPDVRSLKFLDRLVADSRAVALNHTAGLSTPQQVQMTLFSLFALMDESDQYKHTLKQLIRRREATLYRELGTPPQRDENAVDYYTLIDLQDVTSKLYGEAFSKWAVKQSSTGDMLFRIADETGIVLLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRQMADELYAQYTQ 528
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....hhh.eeeeeehhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhh.....eeeeee.hhhhh...hhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh....eeeee..hhhhh....hhhhhh...eeeeee......hhhhh.eeeeee..hhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.........eeeee....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fdd A  27 DGNRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAESELSYSYMNTVGVGGLAKIEGIEGRFERYIAENRDQEGVRFLGKSLSYVRDQLGLDPAAFLHEMVDGILGCNYPVPPRMLNISEKIVRQYIIREMGADAIPSESVNLFAVEGGTAAMAYIFESMKVNGLLKAGDKVAIGMPVFTPYIEIPELAQYALEEVAINADPALNWQYPDSELDKLKDPAIKIFFCVNPSNPPSVKMDERSLERVRKIVAEHRPDLMILTDDVYGTFADGFQSLFAICPANTLLVYSFSKYFGATGWRLGVVAAHKENIFDLALGRLPESEKTALDDRYRSLLPDVRSLKFLDRLVADSRAVALNHTAGLSTPQQVQMTLFSLFALMDESDQYKHTLKQLIRRREATLYRELGTPPQRDENAVDYYTLIDLQDVTSKLYGEAFSKWAVKQSSTGDMLFRIADETGIVLLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRQMADELYAQYTQ 528
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526
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  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 3FDD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q845W8_COMTE | Q845W8)
molecular function
    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.

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