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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL ARG49 PHOSPHOLIPASE A2 HOMOLOGUE FROM ZHAOERMIA MANGSHANENSIS VENOM
 
Authors :  M. T. Murakami, U. Kuch, D. Mebs, R. K. Arni
Date :  10 Apr 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Snake Venom, Arg49, Phospholipase A2, Myotoxin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Murakami, U. Kuch, C. Betzel, D. Mebs, R. K. Arni
Crystal Structure Of A Novel Myotoxic Arg49 Phospholipase A(2) Homolog (Zhaoermiatoxin) From Zhaoermia Mangshanensis Snake Venom: Insights Into Arg49 Coordination And The Role Of Lys122 In The Polarization Of The C-Terminus.
Toxicon V. 51 723 2008
PubMed-ID: 18295812  |  Reference-DOI: 10.1016/J.TOXICON.2007.11.018

(-) Compounds

Molecule 1 - ZHAOERMIATOXIN
    Chains: A, B
    Organism Scientific: ZHAOERMIA MANGSHANENSIS
    Organism Taxid: 242058
    Secretion: VENOM
    Synonym: PHOSPHOLIPASE A2 HOMOLOG

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
2SO410Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:32 , ARG A:34 , ARG A:49 , HOH A:474 , HOH A:486 , PHE B:119BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREARG A:34 , LYS A:53BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREARG B:34 , ARG B:49 , HOH B:484BINDING SITE FOR RESIDUE SO4 B 303
4AC4SOFTWARELYS A:69 , TYR B:21 , LYS B:115 , ARG B:118 , HOH B:458BINDING SITE FOR RESIDUE SO4 B 304
5AC5SOFTWARELYS A:132 , CYS A:133 , HOH A:449 , ARG B:34 , LYS B:53BINDING SITE FOR RESIDUE SO4 B 305
6AC6SOFTWAREHOH A:424 , HOH A:459BINDING SITE FOR RESIDUE PEG A 401
7AC7SOFTWAREPRO B:18 , TYR B:22 , THR B:23 , HOH B:491BINDING SITE FOR RESIDUE PEG B 402

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:27 -A:126
2A:29 -A:45
3A:44 -A:105
4A:50 -A:133
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96
8B:27 -B:126
9B:29 -B:45
10B:44 -B:105
11B:50 -B:133
12B:51 -B:98
13B:61 -B:91
14B:84 -B:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PH4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PH4)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H_PROMB43-50
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H_PROMB85-95
 		  2A:95-105
B:95-105
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H_PROMB43-50
 		  2A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H_PROMB85-95
 		  2A:95-105
B:95-105
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA2H_PROMB43-50
 		  4A:44-51
B:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA2H_PROMB85-95
 		  4A:95-105
B:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 2PH4)

(-) 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:121
 aligned with PA2H_PROMB | P84776 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           PA2H_PROMB     1 SLIELTKMVFQETGKNPVTYYTLYGCNCGVGRRGKPKDATDRCCFVHRCCYKKLTGCDPKKDRYSYSWENKAIVCGEKNPCLKELCECDKAVAICLRKNLGTYDKNYRFTMKFLCDKPEKC 121
               SCOP domains d2ph4a_ A: automated matches                                                                                              SCOP domains
               CATH domains 2ph4A00 A:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh............eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ph4 A   1 SLIELTKMVFQETGKNPVTYYTLYGCNCGVGRRGKPKDATDRCCFVHRCCYKKLTGCDPKKDRYSYSWENKAIVCGEKNPCLKELCECDKAVAICLRKNLGTYDKNYRFTMKFLCDKPEKC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129    


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H_PROMB | P84776 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           PA2H_PROMB     1 SLIELTKMVFQETGKNPVTYYTLYGCNCGVGRRGKPKDATDRCCFVHRCCYKKLTGCDPKKDRYSYSWENKAIVCGEKNPCLKELCECDKAVAICLRKNLGTYDKNYRFTMKFLCDKPEKC 121
               SCOP domains d2ph4b_ B: automated matches                                                                                              SCOP domains
               CATH domains 2ph4B00 B:1-133 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh.............ee....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ph4 B   1 SLIELTKMVFQETGKNPVTYYTLYGCNCGVGRRGKPKDATDRCCFVHRCCYKKLTGCDPKKDRYSYSWENKAIVCGEKNPCLKELCECDKAVAICLRKNLGTYDKNYRFTMKFLCDKPEKC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129
   Legend:   → Mismatch (orange background)
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  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 2PH4)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PA2H_PROMB | P84776)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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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