1Y75 - JenaLib

Title :   A NEW FORM OF CATALYTICALLY INACTIVE PHOSPHOLIPASE A2 WITH AN UNUSUAL DISULPHIDE BRIDGE CYS 32- CYS 49 REVEALS RECOGNITION FOR N-ACETYLGLUCOSMINE

Authors :   T. Jabeen, N. Singh, J. Jasti, R. K. Singh, S. Sharma, M. Perbandt, C. Bet P. Kaur, A. Srinivasan, T. P. Singh

Date :   08 Dec 04 (Deposition) - 03 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A,B  (2x)

Keywords :   Enzyme, Activity, Molecular Association, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Jabeen, N. Singh, R. K. Singh, J. Jasti, S. Sharma, P. Kaur, A. Srinivasan, T. P. Singh
Crystal Structure Of A Heterodimer Of Phospholipase A2 From Naja Naja Sagittifera At 2. 3 A Resolution Reveals The Presence Of A New Pla2-Like Protein With A Novel Cys 32-Cys 49 Disulphide Bridge With A Bound Sugar At The Substrate-Binding Site
Proteins V. 62 329 2006
PubMed-ID: 16287060 | Reference-DOI: 10.1002/PROT.20708

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (15, 15)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A5_NAJSG	49-56	1	A:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A6_NAJSG	49-56	1	B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A6_NAJSG	95-105	1	B:90-100

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A5_NAJSG	49-56	1	A:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A6_NAJSG	49-56	1	B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A6_NAJSG	95-105	1	B:90-100

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A5_NAJSG	49-56	2	A:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A6_NAJSG	49-56	2	B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A6_NAJSG	95-105	2	B:90-100

Biological Unit 3 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A5_NAJSG	49-56	2	A:44-51
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A6_NAJSG	49-56	2	B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A6_NAJSG	95-105	2	B:90-100

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:118
 aligned with PA2A5_NAJSG | Q5G291 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:118
                                    17        27        37        47        57        67        77        87        97       107       117        
          PA2A5_NAJSG     8 NTYQFRNMIQCTVPSRSWWDFADYGCYCGCGSGTPVDDLDRCCQVHCNCYRQAGEISGCRPKFKTYTYECSGGTLTCKGDNNACAASSCDCDRLAAICFAGAPYNDNNYNIDLKARCN 125
               SCOP domains d1y75a_ A: automated matches                                                                                           SCOP domains
               CATH domains 1y75A00 A:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh..............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1y75 A   1 NTYQFRNMIQCTVPSRSWWDFADYGCYCGCGSGTPVDDLDRCCQVHCNCYRQAGEISGCRPKFKTYTYECSGGTLTCKGDNNACAASSCDCDRLAAICFAGAPYNDNNYNIDLKARCN 120
                                    10    ||  21        32        42        52        62        72        82        92       102       112        
                                         15|           30|                                                                                        
                                          17            32

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PA2A6_NAJSG | Q5G290 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:118
                                    17        27        37        47        57        67        77        87        97       107       117        
          PA2A6_NAJSG     8 NIKQFNNMIQCTVPARSWWDFADYGCYCGSGSGSPVDDLDRCCQVHDNCYNAGGGVTGCAPKSKTYTYECSQGTLTCSGENSACAATVCDCDRLAAICFAGAPYNDNNYNIDLKSRCQ 125
               SCOP domains d1y75b_ B: automated matches                                                                                           SCOP domains
               CATH domains 1y75B00 B:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh.............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------PA2_HIS --------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) ---------------------------------------------------------------------------------------PA2_ASP    -------------------- PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1y75 B   1 NIKQFNNMIQCTVPARSWWDFADYGCYCGSGSGSPVDDLDRCCQVHDNCYNAGGGVTGCAPKSKTYTYECSQGTLTCSGENSACAATVCDCDRLAAICFAGAPYNDNNYNIDLKSRCQ 120
                                    10    ||  21        31|       42        52        62        72        82        92       102       112        
                                         15|            31|                                                                                       
                                          17             33

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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (PA2A5_NAJSG | Q5G291)

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.

Chain B (PA2A6_NAJSG | Q5G290)

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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y75)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1y75
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PA2A5_NAJSG \| Q5G291
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PA2A6_NAJSG \| Q5G290
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.1.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description