2WQ5 - JenaLib

Title :   NON-ANTIBIOTIC PROPERTIES OF TETRACYCLINES: STRUCTURAL BASIS FOR INHIBITION OF SECRETORY PHOSPHOLIPASE A2.

Authors :   D. Dalm, G. J. Palm, W. Hinrichs

Date :   13 Aug 09 (Deposition) - 23 Mar 10 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Hydrolase, Minocycline, Phospholipase, Metal-Binding, Lipid Degradation, Calcium Binding Loop, Carboxylic Ester Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Dalm, G. J. Palm, A. Aleksandrov, T. Simonson, W. Hinrichs
Non-Antibiotic Properties Of Tetracyclines: Structural Basi For Inhibition Of Secretory Phospholipase A(2).
J. Mol. Biol. V. 398 83 2010
PubMed-ID: 20211188 | Reference-DOI: 10.1016/J.JMB.2010.02.049

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MIY	1	Ligand/Ion	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MIY	3	Ligand/Ion	(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
3	SO4	3	Ligand/Ion	SULFATE ION

Sites (3, 3)

SS Bonds (7, 7)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJNA	43-50	1	A:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJNA	89-99	1	A:89-99

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJNA	43-50	3	A:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJNA	89-99	3	A:89-99

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:119
 aligned with PA2A2_NAJNA | P15445 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
          PA2A2_NAJNA     1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
               SCOP domains d2wq5a_ A: automated matches                                                                                            SCOP domains
               CATH domains 2wq5A00 A:1-119 Phospholipase A2                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh...............hhhhhhhhhhhhhhhhhh.....hhhhh...eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2wq5 A   1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISKCWPFFKTYSYKCSQGTLTCKGGNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
                                    10        20        30        40        50        60        70        80        90       100       110

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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (PA2A2_NAJNA | P15445)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0004623	phospholipase A2 activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	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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Biological Unit
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