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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE
 
Authors :  B. A. Yard, L. G. Carter, K. A. Johnson, I. M. Overton, S. A. Mcmahon, M. Do H. Liu, D. Puech, M. Oke, G. J. Barton, J. H. Naismith, D. J. Campopiano
Date :  07 Feb 07  (Deposition) - 01 May 07  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Spt, Plp, Sspf, Transferase, Sphingolipid, Pyridoxal Phosphate, Serine Palmitoyl Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Yard, L. G. Carter, K. A. Johnson, I. M. Overton, M. Dorward, H. Liu S. A. Mcmahon, M. Oke, D. Puech, G. J. Barton, J. H. Naismith, D. J. Campopiano
The Structure Of Serine Palmitoyltransferase; Gateway To Sphingolipid Biosynthesis.
J. Mol. Biol. V. 370 870 2007
PubMed-ID: 17559874  |  Reference-DOI: 10.1016/J.JMB.2007.04.086

(-) Compounds

Molecule 1 - SERINE PALMITOYLTRANSFERASE
    Chains: A
    EC Number: 2.3.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: HMS 174 (DES)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS PAUCIMOBILIS
    Organism Taxid: 13689
    Other Details: PLP FORMING INTERNAL ALDIMINE WITH LYS265

 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
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:134 , TYR A:135 , ASN A:138 , HIS A:159 , SER A:161 , 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:2290BINDING SITE FOR RESIDUE PLP A1265
2AC2SOFTWAREHOH A:2030 , HOH A:2062 , HOH A:2064 , HOH A:2102 , HOH A:2104BINDING SITE FOR RESIDUE MG A1421

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JG2)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JG2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JG2)

(-) Exons   (0, 0)

(no "Exon" information available for 2JG2)

(-) 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:399
 aligned with Q93UV0_SPHPI | Q93UV0 from UniProtKB/TrEMBL  Length:420

    Alignment length:399
                                    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 RDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEAVIRGKDTILLGTYNYMGMTFDPDVIAAGKEALEKFGSGTNGSRMLNGTFHDHMEVEQALRDFYGTTGAIVFSTGYMANLGIISTLAGKGEYVILDADSHASIYDGCQQGNAEIVRFRHNSVEDLDKRLGRLPKEPAKLVVLEGVYSMLGDIAPLKEMVAVAKKHGAMVLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSKSVGTVGGFVVSNHPKFEAVRLACRPYIFTASLPPSVVATATTSIRKLMTAHEKRERLWSNARALHGGLKAMGFRLGTETCDSAIVAVMLEDQEQAAMMWQALLDGGLYVNMARPPATPAGTFLLRCSICAEHTPAQIQTVLGMFQAAGRAVGVIG 420
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...........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.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jg2 A  22 RDLLSKFDGLIAERQKLLDSGVTDPFAIVMEQVKSPTEAVIRGKDTILLGTYNYMGMTFDPDVIAAGKEALEKFGSGTNGSRMLNGTFHDHMEVEQALRDFYGTTGAIVFSTGYMANLGIISTLAGKGEYVILDADSHASIYDGCQQGNAEIVRFRHNSVEDLDKRLGRLPKEPAKLVVLEGVYSMLGDIAPLKEMVAVAKKHGAMVLVDEAHSMGFFGPNGRGVYEAQGLEGQIDFVVGTFSKSVGTVGGFVVSNHPKFEAVRLACRPYIFTASLPPSVVATATTSIRKLMTAHEKRERLWSNARALHGGLKAMGFRLGTETCDSAIVAVMLEDQEQAAMMWQALLDGGLYVNMARPPATPAGTFLLRCSICAEHTPAQIQTVLGMFQAAGRAVGVIG 420
                                    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)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2JG2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JG2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JG2)

(-) 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

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

(-) Related Entries Specified in the PDB File

2jgt HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE