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(-) Description

Title :  CRYSTAL STRUCTURE OF L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE FROM S. ENTERICA COMPLEXED WITH ITS REACTION INTERMEDIATE
 
Authors :  C. -G. Cheong, J. Escalante-Semerena, I. Rayment
Date :  05 Apr 02  (Deposition) - 28 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cobd, L-Threonine-O-3-Phosphate, Plp-Dependent Decarboxylase, Cobalamin, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Cheong, J. C. Escalante-Semerena, I. Rayment
Structural Studies Of The L-Threonine-O-3-Phosphate Decarboxylase (Cobd) Enzyme From Salmonella Enterica: The Apo, Substrate, And Product-Aldimine Complexes.
Biochemistry V. 41 9079 2002
PubMed-ID: 12119022  |  Reference-DOI: 10.1021/BI020294W

(-) Compounds

Molecule 1 - L-THREONINE-O-3-PHOSPHATE DECARBOXYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(JE4094)
    Expression System Taxid: 562
    Gene: COBD
    Organism Scientific: SALMONELLA ENTERICA
    Organism Taxid: 28901
    Synonym: COBD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
133P1Ligand/Ion{3-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-PROPYL}-PHOSPHONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
133P2Ligand/Ion{3-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-PROPYL}-PHOSPHONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:8 , GLY A:9 , TYR A:56 , GLY A:84 , GLU A:85 , THR A:86 , PHE A:108 , CYS A:153 , ASN A:157 , ASP A:185 , ALA A:187 , PHE A:188 , SER A:213 , THR A:215 , LYS A:216 , ARG A:224 , ARG A:323 , TYR A:328 , ARG A:337 , HOH A:1014 , HOH A:1028BINDING SITE FOR RESIDUE 33P A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LC8)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:105 -Pro A:106
2Thr A:154 -Pro A:155
3Asn A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LC8)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.COBD_SALTY213-226  1A:213-226
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.COBD_SALTY213-226  2A:213-226

(-) Exons   (0, 0)

(no "Exon" information available for 1LC8)

(-) 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:356
 aligned with COBD_SALTY | P97084 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:356
                                    16        26        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      
           COBD_SALTY     7 AHGGNIREAATVLGISPDQLLDFSANINPLGMPVSVKRALIDNLDCIERYPDADYFHLHQALARHHQVPASWILAGNGETESIFTVASGLKPRRAMIVTPGFAEYGRALAQSGCEIRRWSLREADGWQLTDAILEALTPDLDCLFLCTPNNPTGLLPERPLLQAIADRCKSLNINLILDEAFIDFIPHETGFIPALKDNPHIWVLRSLTKFYAIPGLRLGYLVNSDDAAMARMRRQQMPWSVNALAALAGEVALQDSAWQQATWHWLREEGARFYQALCQLPLLTVYPGRANYLLLRCEREDIDLQRRLLTQRILIRSCANYPGLDSRYYRVAIRSAAQNERLLAALRNVLTGIAP 362
               SCOP domains d1lc8a_ A: L-threonine-O-3-phosphate decarboxylase CobD                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1lc8A01 A:8-37,A:263-362      1lc8A02 A:38-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                             1lc8A01 A:8-37,A:263-362 Aspartate Aminotransferase, domain 1                                        CATH domains
               Pfam domains -----------------Aminotran_1_2-1lc8A01 A:24-353                                                                                                                                                                                                                                                                                                            --------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.hhhhhee..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhh.eeee..hhhhhhhhhhhh...eeeeee...hhhhhhhhhh..eeeeee.hhhhh.....hhhhhh.....eeeee..........hhhhhhhhhhhhhhhh.eeeee..hhhhh.....hhhhh.....eeeeee............eeee..hhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eee......eeeeee.....hhhhhhhh..ee.ee..........eeeee..hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lc8 A   7 AHGGNIREPATVLGISPDQLLDFSANINPLGMPVSVKRALIDNLDCIERYPDADYFHLHQALARHHQVPASWILAGNGETESIFTVASGLKPRRAMIVTPGFAEYGRALAQSGCEIRRWSLREADGWQLTDAILEALTPDLDCLFLCTPNNPTGLLPERPLLQAIADRCKSLNINLILDEAFIDFIPHETGFIPALKDNPHIWVLRSLTKFYAIPGLRLGYLVNSDDAAMARMRRQQMPWSVNALAALAGEVALQDSAWQQATWHWLREEGARFYQALCQLPLLTVYPGRANYLLLRCEREDIDLQRRLLTQRILIRSCANYPGLDSRYYRVAIRSAAQNERLLAALRNVLTGIAP 362
                                    16        26        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
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (COBD_SALTY | P97084)
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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0048472    threonine-phosphate decarboxylase activity    Catalysis of the reaction: O-phospho-L-threonine + H(+) = (R)-1-aminopropan-2-yl phosphate + CO(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:0009236    cobalamin biosynthetic process    The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

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  1lc8
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 Related Entries

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

UniProtKB/Swiss-Prot
        COBD_SALTY | P97084: 1lc5 1lc7 1lkc

(-) Related Entries Specified in the PDB File

1kus SAME PROTEIN, WILD TYPE
1lc5
1lc7