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(-) Description

Title :  INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL DECARBOXYLATIVE MECHANISM OF INACTIVATION
 
Authors :  J. Lowther, B. A. Yard, K. A. Johnson, L. G. Carter, V. T. Bhat, M. C. C. Raman, D. J. Clarke, B. Ramakers, S. A. Mcmahon, J. H. Naismith, D. J. Campopiano
Date :  13 Apr 10  (Deposition) - 19 May 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lowther, B. A. Yard, K. A. Johnson, L. G. Carter, V. T. Bhat, M. C. C. Raman, D. J. Clarke, B. Ramakers, S. A. Mcmahon, J. H. Naismith, D. J. Campopiano
Inhibition Of The Plp-Dependent Enzyme Serine Palmitoyltransferase By Cycloserine: Evidence For A Novel Decarboxylative Mechanism Of Inactivation.
Mol. Biosystems V. 6 1682 2010
PubMed-ID: 20445930  |  Reference-DOI: 10.1039/C003743E

(-) Compounds

Molecule 1 - SERINE PALMITOYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 2-420
    Organism Scientific: SPHINGOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Synonym: SPT, SPT1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PMP1Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2015 , HOH A:2016 , HOH A:2034 , HOH A:2061 , HOH A:2063BINDING SITE FOR RESIDUE MG A1421
2AC2SOFTWAREGLY A:134 , TYR A:135 , ASN A:138 , HIS A:159 , GLU A:202 , ASP A:231 , HIS A:234 , THR A:262 , SER A:264 , LYS A:265 , GLY A:271 , THR A:294 , ALA A:295 , HOH A:2298BINDING SITE FOR RESIDUE PMP A1420

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XBN)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:379 -Pro A:380

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:398
 aligned with Q93UV0_SPHPI | Q93UV0 from UniProtKB/TrEMBL  Length:420

    Alignment length:398
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411        
         Q93UV0_SPHPI    22 RDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEAVIRGKDTILLGTYNYMGMTFDPDVIAAGKEALEKFGSGTNGSRMLNGTFHDHMEVEQALRDFYGTTGAIVFSTGYMANLGIISTLAGKGEYVILDADSHASIYDGCQQGNAEIVRFRHNSVEDLDKRLGRLPKEPAKLVVLEGVYSMLGDIAPLKEMVAVAKKHGAMVLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSKSVGTVGGFVVSNHPKFEAVRLACRPYIFTASLPPSVVATATTSIRKLMTAHEKRERLWSNARALHGGLKAMGFRLGTETCDSAIVAVMLEDQEQAAMMWQALLDGGLYVNMARPPATPAGTFLLRCSICAEHTPAQIQTVLGMFQAAGRAVGVI 419
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhh...eeee..eeee..eeeee.......hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhh......eeeeee.ee....ee.hhhhhhhhhhhh..eeeee.............hhhhhh.......eeeee.........eeeee...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee........eeeeee.hhhhhhhhhhhhhhh.ee.eee.........eeeeee.....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xbn A  22 RDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEAVIRGKDTILLGTYNYMGMTFDPDVIAAGKEALEKFGSGTNGSRMLNGTFHDHMEVEQALRDFYGTTGAIVFSTGYMANLGIISTLAGKGEYVILDADSHASIYDGCQQGNAEIVRFRHNSVEDLDKRLGRLPKEPAKLVVLEGVYSMLGDIAPLKEMVAVAKKHGAMVLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSKSVGTVGGFVVSNHPKFEAVRLACRPYIFTASLPPSVVATATTSIRKLMTAHEKRERLWSNARALHGGLKAMGFRLGTETCDSAIVAVMLEDQEQAAMMWQALLDGGLYVNMARPPATPAGTFLLRCSICAEHTPAQIQTVLGMFQAAGRAVGVI 419
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   Legend:   → Mismatch (orange background)
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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 2XBN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XBN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XBN)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q93UV0_SPHPI | Q93UV0)
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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/TrEMBL
        Q93UV0_SPHPI | Q93UV0: 2jg2 2jgt 2w8j 2w8t 2w8u 2w8v 2w8w 4bmk

(-) Related Entries Specified in the PDB File

2jg2 HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE
2jgt HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE
2w8j SPT WITH PLP-SER
2w8t SPT WITH PLP, N100C
2w8u SPT WITH PLP, N100Y
2w8v SPT WITH PLP, N100W
2w8w N100Y SPT WITH PLP-SER