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(-) Description

Title :  CRYSTAL STRUCTURE OF A CARBOHYDRATE INDUCED DIMER OF GROUP I PHOSPHOLIPASE A2 FROM BUNGARUS CAERULEUS AT 2.1 A RESOLUTION
 
Authors :  G. Singh, S. Gourinath, S. Sharma, S. Bhanumathi, C. Betzel, A. Srinivasan, T. P. Singh
Date :  26 Jul 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Phospholipase A2, Homodimer, Bungarus Caeruleus, Mannose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Singh, S. Gourinath, K. Sarvanan, S. Sharma, S. Bhanumathi, C. Betzel, S. Yadav, A. Srinivasan, T. P. Singh
Crystal Structure Of A Carbohydrate Induced Homodimer Of Phospholipase A(2) From Bungarus Caeruleus At 2. 1A Resolution
J. Struct. Biol. V. 149 264 2005
PubMed-ID: 15721580  |  Reference-DOI: 10.1016/J.JSB.2004.11.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2 ISOFORM 2
    Chains: A, B
    EC Number: 3.1.1.4
    Fragment: RESIDUES 1-120
    Organism Scientific: BUNGARUS CAERULEUS
    Organism Taxid: 132961

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CL2Ligand/IonCHLORIDE ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3MAN2Ligand/IonALPHA-D-MANNOSE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3MAN-1Ligand/IonALPHA-D-MANNOSE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:30 , TYR A:31 , GLY A:32 , ASP A:49 , NA A:1002 , HOH A:1097 , TYR B:31 , GLY B:32 , ASP B:49 , NA B:1001 , MAN B:1009 , HOH B:1112 , HOH B:1114 , HOH B:1115BINDING SITE FOR RESIDUE MAN B 1008
2AC2SOFTWARELEU A:2 , LEU A:64 , TYR B:31 , LEU B:64 , MAN B:1008 , HOH B:1077 , HOH B:1110BINDING SITE FOR RESIDUE MAN B 1009
3AC3SOFTWARETYR B:28 , GLY B:30 , TYR B:31 , GLY B:32 , ASP B:49 , MAN B:1008BINDING SITE FOR RESIDUE NA B 1001
4AC4SOFTWARETYR A:28 , GLY A:30 , TYR A:31 , GLY A:32 , ASP A:49 , MAN B:1008BINDING SITE FOR RESIDUE NA A 1002
5AC5SOFTWARETHR B:82 , SER B:83 , HOH B:1067BINDING SITE FOR RESIDUE CL B 1003
6AC6SOFTWARETHR A:82 , SER A:83 , HOH A:1047BINDING SITE FOR RESIDUE CL A 1004
7AC7SOFTWAREALA A:12 , PRO A:75 , ILE A:99BINDING SITE FOR RESIDUE ACY A 1005
8AC8SOFTWARETHR A:67 , SER A:69 , ASP A:81 , ASP A:84 , THR A:117BINDING SITE FOR RESIDUE ACY A 1006
9AC9SOFTWARETHR B:67 , TYR B:68 , SER B:69 , ASP B:81 , ASP B:84 , THR B:117 , HOH B:1086BINDING SITE FOR RESIDUE ACY B 1007

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:11 -A:72
2A:27 -A:119
3A:29 -A:45
4A:44 -A:100
5A:51 -A:93
6A:61 -A:86
7A:79 -A:91
8B:11 -B:72
9B:27 -B:119
10B:29 -B:45
11B:44 -B:100
12B:51 -B:93
13B:61 -B:86
14B:79 -B:91

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:74 -Pro A:75
2Lys B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U4J)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B5_BUNCE61-68
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B5_BUNCE107-117
 		  2A:90-100
B:90-100
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B5_BUNCE61-68
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B5_BUNCE107-117
 		  2A:90-100
B:90-100
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2B5_BUNCE61-68
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2B5_BUNCE107-117
 		  2A:90-100
B:90-100

(-) Exons   (0, 0)

(no "Exon" information available for 1U4J)

(-) 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 PA2B5_BUNCE | Q6SLM1 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          PA2B5_BUNCE    20 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 137
               SCOP domains d1u4ja_ A: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1u4jA00 A:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1u4j A   1 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 120
                                    10   ||   22        32        42        52        62        72        82        92       102       112        
                                        14|                                                                                                       
                                         17                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PA2B5_BUNCE | Q6SLM1 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          PA2B5_BUNCE    20 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 137
               SCOP domains d1u4jb_ B: Snake phospholipase A2                                                                                      SCOP domains
               CATH domains 1u4jB00 B:1-120 Phospholipase A2                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhh................hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1u4j B   1 NLKQFKNMIQCAGTRTWTSYIGYGCYCGYGGSGTPVDELDRCCYTHDHCYNKAANIPGCNPLIKTYSYTCTKPNITCNDTSDSCARFICDCDRTAAICFASAPYNINNIMISASTSCQ 120
                                    10   ||   22        32        42        52        62        72        82        92       102       112        
                                        14|                                                                                                       
                                         17
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U4J)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PA2B5_BUNCE | Q6SLM1)
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.
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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        PA2B5_BUNCE | Q6SLM1: 1g0z

(-) Related Entries Specified in the PDB File

1fe5 SEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM COMMON KRAIT (BUNGARUS CAERULEUS) AT 2.4 RESOLUTION: IDENTIFICATION AND CHARACTERIZATION OF ITS PHARMACOLOGICAL SITES.