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(-) Description

Title :  CRYSTAL STRUCTURE OF STSPL (SYMMETRIC FORM)
 
Authors :  F. Bourquin, M. G. Grutter, G. Capitani
Date :  23 Mar 10  (Deposition) - 18 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Carboxy-Lyase Activity, Pyridoxal Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Bourquin, H. Riezman, G. Capitani, M. G. Grutter
Structure And Function Of Sphingosine-1-Phosphate Lyase, A Key Enzyme Of Sphingolipid Metabolism.
Structure V. 18 1054 2010
PubMed-ID: 20696404  |  Reference-DOI: 10.1016/J.STR.2010.05.011

(-) Compounds

Molecule 1 - SPHINGOSINE-1-PHOSPHATE LYASE
    Chains: A, B
    EC Number: 4.1.2.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector: PQE70
    Expression System Vector Type: PLASMID
    Gene: STH1274
    Organism Scientific: SYMBIOBACTERIUM THERMOPHILUM
    Organism Taxid: 2734

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:102 , ALA A:103 , TYR A:105 , LLP A:311 , HOH A:580 , HOH A:672 , HOH A:687 , ASN B:126 , HIS B:129 , SER B:353BINDING SITE FOR RESIDUE PO4 A 514
2AC2SOFTWAREASN A:126 , HIS A:129 , GLY B:102 , ALA B:103 , TYR B:105 , LLP B:311BINDING SITE FOR RESIDUE PO4 B 514

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:246 -Pro A:247
2Arg A:436 -Pro A:437
3Ala B:246 -Pro B:247
4Arg B:436 -Pro B:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MAD)

(-) Sequences/Alignments

Asymmetric/Biological 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:451
 aligned with Q67PY4_SYMTH | Q67PY4 from UniProtKB/TrEMBL  Length:507

    Alignment length:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           507 
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507 
         Q67PY4_SYMTH    58 KPYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHGDEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAGGTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKAAQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGYPHGVVDPIPEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSADTHKYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGLYFSPTFAGSRPGALSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWVIAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVLTGFIDLLYEV-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee......hhhhhhhh...............eeee............eeeee.hhhhhh...eee.......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......eeeee....hhhhhhhhhhh.....eee....eeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mad A  58 KPYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHGDEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAGGTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKAAQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGYPHGVVDPIPEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSADTHkYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGLYFSPTFAGSRPGALSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWVIAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVLTGFIDLLYEVH 508
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307   |   317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507 
                                                                                                                                                                                                                                                                                       311-LLP                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:451
 aligned with Q67PY4_SYMTH | Q67PY4 from UniProtKB/TrEMBL  Length:507

    Alignment length:451
                                    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 
         Q67PY4_SYMTH    57 IKPYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHGDEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAGGTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKAAQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGYPHGVVDPIPEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSADTHKYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGLYFSPTFAGSRPGALSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWVIAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVLTGFIDLLYEV 507
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------Pyridoxal_deC-3madB01 B:101-408                                                                                                                                                                                                                                                                                     --------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Pyridoxal_deC-3madB02 B:101-408                                                                                                                                                                                                                                                                                     --------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeeee.....hhhhhhhh...............eeee............eeeee.hhhhhh...eee.......eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee......eeeee....hhhhhhhhhhh.....eee....eeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mad B  57 IKPYRDRFPSHARLPRAGLPRAEILAEIAAMGAAESPAWRDGYASGAVYHGDEHHIAFLNEVYALQSQSNPLHPDLWPSTAKFEAEVVAMTAHMLGGDAAGGTVCGTVTSGGTESLLLAMKTYRDWARATKGITAPEAVVPVSAHAAFDKAAQYFGIKLVRTPLDADYRADVAAMREAITPNTVVVAGSAPGYPHGVVDPIPEIAALAAEHGIGCHVDACLGGFILPWAERLGYPVPPFDFRLEGVTSVSADTHkYGYGAKGTSVILYRRPDLLHYQYFIAADWPGGLYFSPTFAGSRPGALSATAWAAMLSLGEEGYLDATRRILQAADRLKAGVRAIPSLKILGDPLWVIAVASDELNIYQVMEEMAGRGWRLNGLHRPPAFHVALTLRHTEPGVVDRFLADLQDAVAQVRAHPEKATGMAPVYGMAAAAPPELVRQVLTGFIDLLYEV 507
                                    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 
                                                                                                                                                                                                                                                                                        311-LLP
   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  (0, 0)

(no "SCOP Domain" information available for 3MAD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q67PY4_SYMTH | Q67PY4)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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.
biological process
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).

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 Related Entries

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

UniProtKB/TrEMBL
        Q67PY4_SYMTH | Q67PY4: 3maf 3mau 3mbb 5eud 5eue

(-) Related Entries Specified in the PDB File

3maf CRYSTAL STRUCTURE OF STSPL (ASYMMETRIC FORM)
3mau CRYSTAL STRUCTURE OF STSPL IN COMPLEX WITH PHOSPHOETHANOLAMINE
3mbb CRYSTAL STRUCTURE OF STSPL (APO FORM, AFTER TREATMENT WITH SEMICARBAZIDE)
3mc6 CRYSTAL STRUCTURE OF SCDPL1