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(-) Description

Title :  CRYSTAL STRUCTURE OF SERINE PALMITOYLTRANSFERASE FROM SPHINGOBACTERIUM MULTIVORUM WITH SUBSTRATE L-SERINE
 
Authors :  A. Okamoto, J. Hoseki
Date :  09 May 09  (Deposition) - 14 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Vitamin B6-Dependent Enzyme Fold Type I, Acyltransferase, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ikushiro, M. M. Islam, A. Okamoto, J. Hoseki, T. Murakawa, S. Fujii, I. Miyahara, H. Hayashi
Structural Insights Into The Enzymatic Mechanism Of Serine Palmitoyltransferase From Sphingobacterium Multivorum
J. Biochem. V. 146 549 2009
PubMed-ID: 19564159  |  Reference-DOI: 10.1093/JB/MVP100

(-) Compounds

Molecule 1 - SERINE PALMITOYLTRANSFERASE
    Chains: A
    EC Number: 2.3.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)(PLYSS)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPT
    Organism Scientific: SPHINGOBACTERIUM MULTIVORUM
    Organism Taxid: 28454
    Strain: GTC97

 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
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SER1Mod. Amino AcidSERINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SER2Mod. Amino AcidSERINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:138 , LYS A:244 , PHE A:272 , ALA A:274 , PLP A:400 , HOH A:510 , HOH A:516 , HOH A:599BINDING SITE FOR RESIDUE SER A 401
2AC2SOFTWARETHR A:112 , GLY A:113 , PHE A:114 , HIS A:138 , SER A:140 , ASP A:181 , ASP A:210 , ALA A:212 , HIS A:213 , MET A:239 , THR A:241 , SER A:243 , LYS A:244 , SER A:273 , ALA A:274 , SER A:401 , HOH A:501 , HOH A:524BINDING SITE FOR RESIDUE PLP A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A2B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:356 -Pro A:357

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A2B)

(-) Exons   (0, 0)

(no "Exon" information available for 3A2B)

(-) 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:393
 aligned with A7BFV6_SPHMU | A7BFV6 from UniProtKB/TrEMBL  Length:399

    Alignment length:396
                                    11        21        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      
         A7BFV6_SPHMU     2 SKGKLGEKISQFKIVEELKAKGLYAYFRPIQSKQDTEVKIDGRRVLMFGSNSYLGLTTDTRIIKAAQDALEKYGTGCAGSRFLNGTLDIHVELEEKLSAYVGKEAAILFSTGFQSNLGPLSCLMGRNDYILLDERDHASIIDGSRLSFSKVIKYGHNNMEDLRAKLSRLPEDSAKLICTDGIFSMEGDIVNLPELTSIANEFDAAVMVDDAHSLGVIGHKGAGTASHFGLNDDVDLIMGTFSKSLASLGGFVAGDADVIDFLKHNARSVMFSASMTPASVASTLKALEIIQNEPEHIEKLWKNTDYAKAQLLDHGFDLGATESPILPIFIRSNEKTFWVTKMLQDDGVFVNPVVSPAVPAEESLIRFSLMATHTYDQIDEAIEKMVKVFKQAEVET 397
               SCOP domains d3a2ba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhh...............eeee..eeeee............hhhhhhhhhhhhhh..............hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeee....hhhhhhhhhh......eeeeee...........hhhhhhhhh....eeeee.........hhh..hhhhh..hhh..eeeee.........eeeee.hhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..........eeeee...hhhhhhhhhhhhhh.ee.eee..........eeeee......hhhhhhhhhhhhhhhhhh---. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a2b A   2 SKGKLGEKISQFKIVEELKAKGLYAYFRPIQSKQDTEVKIDGRRVLMFGSNSYLGLTTDTRIIKAAQDALEKYGTGCAGSRFLNGTLDIHVELEEKLSAYVGKEAAILFSTGFQSNLGPLSCLMGRNDYILLDERDHASIIDGSRLSFSKVIKYGHNNMEDLRAKLSRLPEDSAKLICTDGIFSMEGDIVNLPELTSIANEFDAAVMVDDAHSLGVIGHKGAGTASHFGLNDDVDLIMGTFSKSLASLGGFVAGDADVIDFLKHNARSVMFSASMTPASVASTLKALEIIQNEPEHIEKLWKNTDYAKAQLLDHGFDLGATESPILPIFIRSNEKTFWVTKMLQDDGVFVNPVVSPAVPAEESLIRFSLMATHTYDQIDEAIEKMVKVFKQA---S 401
                                    11        21        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 |   |
                                                                                                                                                                                                                                                                                                                                                                                                                                 393 401
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A2B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A2B)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (A7BFV6_SPHMU | A7BFV6)
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:0004758    serine C-palmitoyltransferase activity    Catalysis of the reaction: L-serine + H(+) + palmitoyl-CoA = 3-dehydrosphinganine + CO(2) + CoA.
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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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