3RLH - JenaLib

Title :   CRYSTAL STRUCTURE OF A CLASS II PHOSPHOLIPASE D FROM LOXOSCELES INTERMEDIA VENOM

Authors :   P. O. Giuseppe, A. Ullah, S. S. Veiga, M. T. Murakami, R. K. Arni

Date :   19 Apr 11 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym./Biol. Unit : A

Keywords :   Class Ii Pld, Tim Beta/Alpha-Barrel Superfamily, Plc-Like Phosphodiesterase, Phospholipase D, Venom, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. O. De Giuseppe, A. Ullah, D. T. Silva, L. H. Gremski, A. C. Wille, D. Chaves Moreira, A. S. Ribeiro, O. M. Chaim, M. T. Murakami, S. S. Veiga, R. K. Arni
Structure Of A Novel Class Ii Phospholipase D: Catalytic Cleft Is Modified By A Disulphide Bridge.
Biochem. Biophys. Res. Commun. V. 409 622 2011
PubMed-ID: 21616057 | Reference-DOI: 10.1016/J.BBRC.2011.05.053

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:32 , ASP A:34 , ASP A:91 , PEG A:289 , PEG A:291 , HOH A:294	BINDING SITE FOR RESIDUE MG A 286
2	AC2	SOFTWARE	ASP A:104 , LYS A:108 , LYS A:111 , HOH A:336 , HOH A:456	BINDING SITE FOR RESIDUE PGE A 287
3	AC3	SOFTWARE	ASN A:137 , LYS A:185	BINDING SITE FOR RESIDUE PEG A 288
4	AC4	SOFTWARE	HIS A:12 , GLU A:32 , ASP A:34 , HIS A:47 , ASP A:91 , LYS A:93 , MG A:286 , HOH A:294 , HOH A:328 , HOH A:369 , HOH A:424	BINDING SITE FOR RESIDUE PEG A 289
5	AC5	SOFTWARE	LYS A:267 , HOH A:450	BINDING SITE FOR RESIDUE PEG A 290
6	AC6	SOFTWARE	HIS A:12 , ASP A:91 , TYR A:228 , TRP A:230 , MG A:286 , HOH A:369 , HOH A:380 , HOH A:424	BINDING SITE FOR RESIDUE PEG A 291
7	AC7	SOFTWARE	GLU A:22 , PHE A:23 , ARG A:55 , ASN A:252	BINDING SITE FOR RESIDUE EDO A 292
8	AC8	SOFTWARE	SER A:96 , TYR A:98	BINDING SITE FOR RESIDUE EDO A 293

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:278
 aligned with A1HA_LOXIN | P0CE80 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:278
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        
           A1HA_LOXIN    28 GNRRPIWIMGHMVNAIGQIDEFVNLGANSIETDVSFDDNANPEYTYHGIPCDCGRNCKKYENFNDFLKGLRSATTPGNSKYQEKLVLVVFDLKTGSLYDNQANDAGKKLAKNLLQHYWNNGNNGGRAYIVLSIPDLNHYPLIKGFKDQLTKDGHPELMDKVGHDFSGNDDIGDVGKAYKKAGITGHIWQSDGITNCLPRGLSRVNAAVANRDSANGFINKVYYWTVDKRSTTRDALDAGVDGIMTNYPDVITDVLNEAAYKKKFRVATYDENPWVTFK 305
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GDPD_2-3rlhA01 A:226-255      ----------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhh...eeeeee...........................hhhhhhhhhhhhh............eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh.eee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rlh A   2 GNRRPIWIMGHMVNAIGQIDEFVNLGANSIETDVSFDDNANPEYTYHGIPCDCGRNCKKYENFNDFLKGLRSATTPGNSKYQEKLVLVVFDLKTGSLYDNQANDAGKKLAKNLLQHYWNNGNNGGRAYIVLSIPDLNHYPLIKGFKDQLTKDGHPELMDKVGHDFSGNDDIGDVGKAYKKAGITGHIWQSDGITNCLPRGLSRVNAAVANRDSANGFINKVYYWTVDKRSTTRDALDAGVDGIMTNYPDVITDVLNEAAYKKKFRVATYDDNPWVTFK 284
                                    11        21        31        40        50        60        70        80        90       100       110       120       130       140       150       160      |175       185       195       205|      216       226       236       246       256       266       276        
                                                                39A                                                                                                                             167|                             205|                                                                             
                                                                                                                                                                                                 173                              207

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A1HA_LOXIN | P0CE80)

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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004630	phospholipase D activity	Catalysis of the reaction: a phosphatidylcholine + H2O = choline + a phosphatidate.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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