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PDBsum entry 1f0i

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Hydrolase PDB id
1f0i
Jmol
Contents
Protein chain
496 a.a. *
Ligands
PO4 ×2
Waters ×699
* Residue conservation analysis
PDB id:
1f0i
Name: Hydrolase
Title: The first crystal structure of a phospholipase d
Structure: Phospholipase d. Chain: a. Ec: 3.1.4.4
Source: Streptomyces sp.. Organism_taxid: 172564. Strain: pmf
Resolution:
1.40Å     R-factor:   0.130     R-free:   0.185
Authors: I.Leiros,F.Secundo,C.Zambonelli,S.Servi,E.Hough
Key ref:
I.Leiros et al. (2000). The first crystal structure of a phospholipase D. Structure, 8, 655-667. PubMed id: 10873862 DOI: 10.1016/S0969-2126(00)00150-7
Date:
16-May-00     Release date:   16-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P84147  (P84147_STRSM) -  Phospholipase D
Seq:
Struc:
506 a.a.
496 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.4.4  - Phospholipase D.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphatidylcholine + H2O = choline + a phosphatidate
phosphatidylcholine
+ H(2)O
= choline
+ phosphatidate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00150-7 Structure 8:655-667 (2000)
PubMed id: 10873862  
 
 
The first crystal structure of a phospholipase D.
I.Leiros, F.Secundo, C.Zambonelli, S.Servi, E.Hough.
 
  ABSTRACT  
 
BACKGROUND: The phospholipase D (PLD) superfamily includes enzymes that are involved in phospholipid metabolism, nucleases, toxins and virus envelope proteins of unknown function. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. PLD also catalyses a transphosphatidylation reaction in the presence of phosphatidylcholine and a short-chained primary or secondary alcohol. RESULTS: The first crystal structure of a 54 kDa PLD has been determined to 1.9 A resolution using the multiwavelength anomalous dispersion (MAD) method on a single WO(4) ion and refined to 1.4 A resolution. PLD from the bacterial source Streptomyces sp. strain PMF consists of a single polypeptide chain that is folded into two domains. An active site is located at the interface between these domains. The presented structure supports the proposed superfamily relationship with the published structure of the 16 kDa endonuclease from Salmonella typhimurium. CONCLUSIONS: The structure of PLD provides insight into the structure and mode of action of not only bacterial, plant and mammalian PLDs, but also of a variety of enzymes as diverse as cardiolipin synthases, phosphatidylserine synthases, toxins, endonucleases, as well as poxvirus envelope proteins having a so far unknown function. The common features of these enzymes are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Topology and tertiary structure of PLD. (a) Overall topology of PLD from Streptomyces sp. strain PMF. Modified figure from TOPS [46]. The N-terminal 260 residues are shown in light blue and the remainder of the protein is colored in dark blue, in order to separate the two domains. (b) Stereographic overview of the tertiary arrangement of the protein. Helices are shown in red and strands in yellow. The protein is viewed from the outer membrane, and the active-site-bound phosphate can be seen in the center of the protein. This Figure was created using BOBSCRIPT. (c) Stereographic presentation of the Ca trace of PLD, made using BOBSCRIPT. The orientation of the protein is as in (b).
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 655-667) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23064230 H.Nishimasu, H.Ishizu, K.Saito, S.Fukuhara, M.K.Kamatani, L.Bonnefond, N.Matsumoto, T.Nishizawa, K.Nakanaga, J.Aoki, R.Ishitani, H.Siomi, M.C.Siomi, and O.Nureki (2012).
Structure and function of Zucchini endoribonuclease in piRNA biogenesis.
  Nature, 491, 284-287.
PDB codes: 4gel 4gem 4gen
21295509 T.Collet, T.Macnaughton, T.Walsh, J.Debattista, and P.Timms (2011).
Identification of novel markers for uncomplicated lower genital tract infections and upper genital tract pathology due to Chlamydia trachomatis.
  Int J Infect Dis, 15, e257-e266.  
21085684 F.Yoshikawa, Y.Banno, Y.Otani, Y.Yamaguchi, Y.Nagakura-Takagi, N.Morita, Y.Sato, C.Saruta, H.Nishibe, T.Sadakata, Y.Shinoda, K.Hayashi, Y.Mishima, H.Baba, and T.Furuichi (2010).
Phospholipase d family member 4, a transmembrane glycoprotein with no phospholipase D activity, expression in spleen and early postnatal microglia.
  PLoS One, 5, e13932.  
19039525 J.R.Simkhada, H.J.Lee, S.Y.Jang, S.S.Cho, E.J.Park, J.K.Sohng, and J.C.Yoo (2009).
A novel alkalo- and thermostable phospholipase D from Streptomyces olivochromogenes.
  Biotechnol Lett, 31, 429-435.  
19333395 S.Sandhya, S.S.Rani, B.Pankaj, M.K.Govind, B.Offmann, N.Srinivasan, and R.Sowdhamini (2009).
Length variations amongst protein domain superfamilies and consequences on structure and function.
  PLoS ONE, 4, e4981.  
18338352 A.Masayama, T.Takahashi, K.Tsukada, S.Nishikawa, R.Takahashi, M.Adachi, K.Koga, A.Suzuki, T.Yamane, H.Nakano, and Y.Iwasaki (2008).
Streptomyces phospholipase D mutants with altered substrate specificity capable of phosphatidylinositol synthesis.
  Chembiochem, 9, 974-981.  
18942690 K.Kuppe, A.Kerth, A.Blume, and R.Ulbrich-Hofmann (2008).
Calcium-induced membrane microdomains trigger plant phospholipase D activity.
  Chembiochem, 9, 2853-2859.  
  18473723 T.S.Dexheimer, S.Antony, C.Marchand, and Y.Pommier (2008).
Tyrosyl-DNA phosphodiesterase as a target for anticancer therapy.
  Anticancer Agents Med Chem, 8, 381-389.  
17221199 L.De Maria, J.Vind, K.M.Oxenbøll, A.Svendsen, and S.Patkar (2007).
Phospholipases and their industrial applications.
  Appl Microbiol Biotechnol, 74, 290-300.  
17192590 P.Schäfer, I.A.Cymerman, J.M.Bujnicki, and G.Meiss (2007).
Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.
  Protein Sci, 16, 82-91.  
17855396 S.H.Chan, Y.Bao, E.Ciszak, S.Laget, and S.Y.Xu (2007).
Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.
  Nucleic Acids Res, 35, 6238-6248.  
17451436 S.Stumpe, S.König, and R.Ulbrich-Hofmann (2007).
Insights into the structure of plant alpha-type phospholipase D.
  FEBS J, 274, 2630-2640.  
17189478 Y.Uesugi, J.Arima, M.Iwabuchi, and T.Hatanaka (2007).
C-terminal loop of Streptomyces phospholipase D has multiple functional roles.
  Protein Sci, 16, 197-207.  
16818490 G.M.Simon, and B.F.Cravatt (2006).
Endocannabinoid biosynthesis proceeding through glycerophospho-N-acyl ethanolamine and a role for alpha/beta-hydrolase 4 in this pathway.
  J Biol Chem, 281, 26465-26472.  
16698554 J.H.Han, N.Kerrison, C.Chothia, and S.A.Teichmann (2006).
Divergence of interdomain geometry in two-domain proteins.
  Structure, 14, 935-945.  
17028579 S.Y.Choi, P.Huang, G.M.Jenkins, D.C.Chan, J.Schiller, and M.A.Frohman (2006).
A common lipid links Mfn-mediated mitochondrial fusion and SNARE-regulated exocytosis.
  Nat Cell Biol, 8, 1255-1262.  
16041402 B.D.Levy, L.Hickey, A.J.Morris, M.Larvie, R.Keledjian, N.A.Petasis, G.Bannenberg, and C.N.Serhan (2005).
Novel polyisoprenyl phosphates block phospholipase D and human neutrophil activation in vitro and murine peritoneal inflammation in vivo.
  Br J Pharmacol, 146, 344-351.  
15973486 R.Ulbrich-Hofmann, A.Lerchner, M.Oblozinsky, and L.Bezakova (2005).
Phospholipase D and its application in biocatalysis.
  Biotechnol Lett, 27, 535-544.  
16247004 S.Grazulis, E.Manakova, M.Roessle, M.Bochtler, G.Tamulaitiene, R.Huber, and V.Siksnys (2005).
Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
  Proc Natl Acad Sci U S A, 102, 15797-15802.
PDB code: 2c1l
15899903 Y.Uesugi, K.Mori, J.Arima, M.Iwabuchi, and T.Hatanaka (2005).
Recognition of phospholipids in Streptomyces phospholipase D.
  J Biol Chem, 280, 26143-26151.  
15326592 C.L.Aikens, A.Laederach, and P.J.Reilly (2004).
Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking.
  Proteins, 57, 27-35.
PDB codes: 1tai 1taj 1tak 1tao 1tav 1tb1 1tb2 1u4t 1u4u 1u4v 1u4w 1u4x 1u4y 1u4z 1u50 1u51 1u52
15052340 M.McDermott, M.J.Wakelam, and A.J.Morris (2004).
Phospholipase D.
  Biochem Cell Biol, 82, 225-253.  
14557260 C.Zambonelli, M.Casali, and M.F.Roberts (2003).
Mutagenesis of putative catalytic and regulatory residues of Streptomyces chromofuscus phospholipase D differentially modifies phosphatase and phosphodiesterase activities.
  J Biol Chem, 278, 52282-52289.  
12519726 C.Zambonelli, and M.F.Roberts (2003).
An iron-dependent bacterial phospholipase D reminiscent of purple acid phosphatases.
  J Biol Chem, 278, 13706-13711.  
12618186 D.R.Davies, H.Interthal, J.J.Champoux, and W.G.Hol (2003).
Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.
  Chem Biol, 10, 139-147.
PDB code: 1nop
11884230 A.J.Melendez, and J.M.Allen (2002).
Phospholipase D and immune receptor signalling.
  Semin Immunol, 14, 49-55.  
11940565 K.El Kirat, F.Besson, A.F.Prigent, J.P.Chauvet, and B.Roux (2002).
Role of calcium and membrane organization on phospholipase D localization and activity. Competition between a soluble and insoluble substrate.
  J Biol Chem, 277, 21231-21236.  
12191592 M.Rizzo, and G.Romero (2002).
Pharmacological importance of phospholipase D and phosphatidic acid in the regulation of the mitogen-activated protein kinase cascade.
  Pharmacol Ther, 94, 35-50.  
12153566 T.J.Cheng, P.G.Rey, T.Poon, and C.C.Kan (2002).
Kinetic studies of human tyrosyl-DNA phosphodiesterase, an enzyme in the topoisomerase I DNA repair pathway.
  Eur J Biochem, 269, 3697-3704.  
11173493 C.Abergel, A.Abousalham, S.Chenivesse, M.Rivière, A.M.Moustacas-Gardies, and R.Verger (2001).
Crystallization and preliminary crystallographic study of a recombinant phospholipase D from cowpea (Vigna unguiculata L. Walp).
  Acta Crystallogr D Biol Crystallogr, 57, 320-322.  
11572945 H.Interthal, J.J.Pouliot, and J.J.Champoux (2001).
The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily.
  Proc Natl Acad Sci U S A, 98, 12009-12014.  
11337397 X.Wang (2001).
PLANT PHOSPHOLIPASES.
  Annu Rev Plant Physiol Plant Mol Biol, 52, 211-231.  
11114512 J.H.Hurley, Y.Tsujishita, and M.A.Pearson (2000).
Floundering about at cell membranes: a structural view of phospholipid signaling.
  Curr Opin Struct Biol, 10, 737-743.  
11106425 Z.Xie, W.T.Ho, and J.H.Exton (2000).
Conserved amino acids at the C-terminus of rat phospholipase D1 are essential for enzymatic activity.
  Eur J Biochem, 267, 7138-7146.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.