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(-) Description

Title :  PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.
 
Authors :  I. Leiros, S. Mcsweeney, E. Hough
Date :  02 Apr 04  (Deposition) - 03 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A
Keywords :  Phospholipase D, Hydrolase, Substrate Soak, Dibutyrylphosphatidylcholine, Dic4Pc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Leiros, S. Mcsweeney, E. Hough
The Reaction Mechanism Of Phospholipase D From Streptomyces Sp. Strain Pmf. Snapshots Along The Reaction Pathway Reveal A Pentacoordinate Reaction Intermediate And An Unexpected Final Product
J. Mol. Biol. V. 339 805 2004
PubMed-ID: 15165852  |  Reference-DOI: 10.1016/J.JMB.2004.04.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE D
    Chains: A
    EC Number: 3.1.4.4
    Organism Scientific: STREPTOMYCES SP.
    Organism Taxid: 172564
    Strain: PMF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HI51Ligand/Ion2-(BUTYRYLOXY)-1-{[(TETRAHYDROXYPHOSPHORANYL)OXY]METHYL}ETHYL BUTYRATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:90 , TRP A:168 , HIS A:170 , LYS A:172 , ASN A:187 , HIS A:448 , LYS A:450 , ASN A:465 , TYR A:467 , HOH A:2413BINDING SITE FOR RESIDUE HI5 A1515

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:55 -A:61
2A:227 -A:246
3A:301 -A:348
4A:423 -A:512

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:52 -Pro A:53
2Ala A:91 -Pro A:92
3Cys A:348 -Pro A:349
4Pro A:349 -Pro A:350

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1V0Y)

(-) 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:493
 aligned with P84147_STRSM | P84147 from UniProtKB/TrEMBL  Length:506

    Alignment length:504
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502    
         P84147_STRSM     3 SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNKLKVRILVGAAPVYHMNVIPSKYRDELTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANRGAVGSGGYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICNA 506
               SCOP domains d1v0ya1 A:6-263 Phospholipase D                                                                                                                                                                                                                                   d1v0ya2 A:264-514 Phospholipase D                                                                                                                                                                                                                      SCOP domains
               CATH domains 1v0yA02 A:6-47,A:264-514                  1v0yA01 A:48-263 Endonuclease Chain A                                                                                                                                                                                   1v0yA02 A:6-47,A:264-514 Endonuclease Chain A                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLDc_2-1v0yA01 A:326-496                                                                                                                                                  ------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh....eeeeeeeee..........eeee...........hhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...-----.hhhhhhhhhhhhhhhhhh.eeeeeeee.............eeee...eeeee....hhhhhh.......eeeeeeehhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhh.........eeeeeeeee...................................hhhhhhhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh..eeeeee.hhhhh------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee...................eeeee...eeeee.........eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v0y A   6 SATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNKLKVRILVGAAP-----VIPSKYRDELTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCQNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANR------GYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICNA 514
                                    15        25        35        45        55        65        75        85        95       105       115       125|     |135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285    || 298   ||  309       319       329       339       349       359       369       379  |    389       399       409      |420       430       440       450       460       470       480       490       500       510    
                                                                                                                                                  126   132                                                                                                                                                           290|     302|                                                                           382    389                        416|                                                                                                
                                                                                                                                                                                                                                                                                                                       294      304                                                                                                              418
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PLD (22)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P84147_STRSM | P84147)
molecular function
    GO:0070290    N-acylphosphatidylethanolamine-specific phospholipase D activity    Catalysis of the release of N-acylethanolamine from N-acyl-phosphatidylethanolamine (NAPE) to generate N-acylethanolamine (NAE).
    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:0004630    phospholipase D activity    Catalysis of the reaction: a phosphatidylcholine + H2O = choline + a phosphatidate.

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 Related Entries

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

UniProtKB/TrEMBL
        P84147_STRSM | P84147: 1f0i 1v0r 1v0s 1v0t 1v0u 1v0v 1v0w

(-) Related Entries Specified in the PDB File

1v0r TUNGSTATE INHIBITED PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN
1v0s UNINHIBITED PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF.
1v0t PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE PRODUCT GLYCEROPHOSPHATE.
1v0u PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE PRODUCT GLYCEROPHOSPHATE.
1v0v PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.
1v0w PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.