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(-) Description

Title :  THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D
 
Authors :  I. Leiros, F. Secundo, C. Zambonelli, S. Servi, E. Hough
Date :  16 May 00  (Deposition) - 16 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Phospholipase D, Alpha-Beta-Alpha-Beta-Alpha Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Leiros, F. Secundo, C. Zambonelli, S. Servi, E. Hough
The First Crystal Structure Of A Phospholipase D.
Structure Fold. Des. V. 8 655 2000
PubMed-ID: 10873862  |  Reference-DOI: 10.1016/S0969-2126(00)00150-7

(-) 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, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:170 , LYS A:172 , ASN A:187 , HIS A:448 , LYS A:450 , ASN A:465 , HOH A:1031 , HOH A:1138 , HOH A:1228 , HOH A:1367 , HOH A:1686BINDING SITE FOR RESIDUE PO4 A 600
2AC2SOFTWAREGLY A:146 , LYS A:147 , HIS A:307 , HOH A:1196 , HOH A:1541BINDING SITE FOR RESIDUE PO4 A 601

(-) 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 1F0I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F0I)

(-) Exons   (0, 0)

(no "Exon" information available for 1F0I)

(-) 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:496
 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 d1f0ia1 A:6-263 Phospholipase D                                                                                                                                                                                                                                   d1f0ia2 A:264-514 Phospholipase D                                                                                                                                                                                                                      SCOP domains
               CATH domains 1f0iA02 A:6-47,A:264-514                  1f0iA01 A:48-263 Endonuclease Chain A                                                                                                                                                                                   1f0iA02 A:6-47,A:264-514 Endonuclease Chain A                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....hhhh.eeee...........hhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...--...hhhhhhhhhhhhhhhhhhh.eeeeeeee.............eeee...eeeee....hhhhhh.......eeeeeeehhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhh.........eeeeeee.....................................hhhhhhhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh..eeeeee.hhhhh------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee...................eeeee...eeeee...........eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f0i A   6 AATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNSLKVRILVGAAP--HMNGIPSKYRDKLTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCKNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANR------GYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICGA 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  |                                                                                                                                                              290|     302|                                                                           382    389                        416|                                                                                                
                                                                                                                                                     129                                                                                                                                                               294      304                                                                                                              418                                                                                                


Chain A from PDB  Type:PROTEIN  Length:496
 aligned with Q93HV1_9ACTN | Q93HV1 from UniProtKB/TrEMBL  Length:542

    Alignment length:504
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538    
         Q93HV1_9ACTN    39 RGAPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDASAADPTDWLLQTPGCWGDDKCAERPGTKRLLAKMTENISKAKRTVDISTLAPFPNGAFQDAIVAGLKSAAESGNKLKVRILVGAAPVYHLNVMPSKYRDELNSKLGKTAGDITLNVASMTTSKTAFSWNHSKLLVVDGQSAITGGINGWKDDYVDTSHPVSDVDLALTGPAAGSAGRYLDQLWSWTCQNKSNVASVWFASSNGADCMPTLQKDANPKAAPATGDVPVIAVGGLGVGIKDKDASSSFSPDLPSASDTKCVVGLHDNTNADRDYDTVNPEESALRALVGSAKKHVEISQQDLNATCPPLPRYDVRLYDAIAAKMAAGVKVRIVVSDPANRGAVGSGGYSQIKSLSEVSDLLRNRLALITGGQQGAKAAMCSNLQLATARSSDSAKWADGKPYAQHHKLVSVDDSAFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLAPQWQYSKASATFDYERGLCQG 542
               SCOP domains d1f0ia1 A:6-263 Phospholipase D                                                                                                                                                                                                                                   d1f0ia2 A:264-514 Phospholipase D                                                                                                                                                                                                                      SCOP domains
               CATH domains 1f0iA02 A:6-47,A:264-514                  1f0iA01 A:48-263 Endonuclease Chain A                                                                                                                                                                                   1f0iA02 A:6-47,A:264-514 Endonuclease Chain A                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....hhhh.eeee...........hhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee...--...hhhhhhhhhhhhhhhhhhh.eeeeeeee.............eeee...eeeee....hhhhhh.......eeeeeeehhhhhhhhhhhhhhhhhhhhh......eeeee........hhhhhhh.........eeeeeee.....................................hhhhhhhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh..eeeeee.hhhhh------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee...................eeeee...eeeee...........eeeeeehhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f0i A   6 AATPHLDAVEQTLRQVSPGLEGDVWERTSGNKLDGSAADPSDWLLQTPGCWGDDKCADRVGTKRLLAKMTENIGNATRTVDISTLAPFPNGAFQDAIVAGLKESAAKGNSLKVRILVGAAP--HMNGIPSKYRDKLTAKLGKAAENITLNVASMTTSKTAFSWNHSKILVVDGQSALTGGINSWKDDYLDTTHPVSDVDLALTGPAAGSAGRYLDTLWTWTCKNKSNIASVWFAASGNAGCMPTMHKDTNPKASPATGNVPVIAVGGLGVGIKDVDPKSTFRPDLPTASDTKCVVGLHDNTNADRDYDTVNPEESALRALVASAKGHIEISQQDLNATCPPLPRYDIRLYDALAAKMAAGVKVRIVVSDPANR------GYSQIKSLSEISDTLRNRLANITGGQQAAKTAMCSNLQLATFRSSPNGKWADGHPYAQHHKLVSVDSSTFYIGSKNLYPSWLQDFGYIVESPEAAKQLDAKLLDPQWKYSQETATVDYARGICGA 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  |                                                                                                                                                              290|     302|                                                                           382    389                        416|                                                                                                
                                                                                                                                                     129                                                                                                                                                               294      304                                                                                                              418
   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  (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  (0, 0)

(no "Pfam Domain" information available for 1F0I)

(-) Gene Ontology  (3, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q93HV1_9ACTN | Q93HV1)
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.

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: 1v0r 1v0s 1v0t 1v0u 1v0v 1v0w 1v0y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1F0I)