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(-) Description

Title :  STRUCTURE OF GAP31
 
Authors :  X. -P. Kong
Date :  26 Nov 09  (Deposition) - 26 Jan 10  (Release) - 16 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Plant Seeds, Glycosidase, Disulfide Bond, Glycoprotein, Hydrolase, Plant Defense, Protein Synthesis Inhibitor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. G. Li, P. L. Huang, D. Zhang, Y. Sun, H. C. Chen, J. Zhang, P. L. Huang, X. P. Kong, S. Lee-Huang
A New Activity Of Anti-Hiv And Anti-Tumor Protein Gap31: Dna Adenosine Glycosidase--Structural And Modeling Insight Into Its Functions.
Biochem. Biophys. Res. Commun. V. 391 340 2010
PubMed-ID: 19913503  |  Reference-DOI: 10.1016/J.BBRC.2009.11.060

(-) Compounds

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN GELONIN
    Chains: A, B
    EC Number: 3.2.2.22
    Fragment: (UNP RESIDUE 47-297)
    Organism Common: EUPHORBIACEAE HIMALAYA
    Organism Scientific: GELONIUM MULTIFLORUM
    Organism Taxid: 3979
    Other Details: ISOLATED FROM SEEDS OF GELONIUM MULTIFLORUM
    Synonym: RRNA N-GLYCOSIDASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:187 , ALA A:188 , ASN A:189 , ALA A:223 , ASN A:224BINDING SITE FOR RESIDUE NAG A 410
2AC2SOFTWAREGLU B:124 , ALA B:188 , ASN B:189 , ASN B:224BINDING SITE FOR RESIDUE NAG B 411

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:44 -A:50
2B:44 -B:50

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KTZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KTZ)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPG_SURMU207-223
 		  2A:161-177
B:161-177
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPG_SURMU207-223
 		  1A:161-177
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RIPG_SURMU207-223
 		  1-
B:161-177

(-) Exons   (0, 0)

(no "Exon" information available for 3KTZ)

(-) 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:251
 aligned with RIPG_SURMU | P33186 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:251
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 
           RIPG_SURMU    47 GLDTVSFSTKGATYITYVNFLNELRVKLKPEGNSHGIPLLRKKCDDPGKCFVLVALSNDNGQLAEIAIDVTSVYVVGYQVRNRSYFFKDAPDAAYEGLFKNTIKTRLHFGGSYPSLEGEKAYRETTDLGIEPLRIGIKKLDENAIDNYKPTEIASSLLVVIQMVSEAARFTFIENQIRNNFQQRIRPANNTISLENKWGKLSFQIRTSGANGMFSEAVELERANGKKYYVTAVDQVKPKIALLKFVDKDPK 297
               SCOP domains d3ktza_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 3ktzA01 A:1-168 Ricin (A subunit), domain 1                                                                                                                             3ktzA02 A:169-251 Ricin (A Subunit), domain 2                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh....ee..ee............eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhh....eeee.....hhhhhhh...hhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeeehhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ktz A   1 GLDTVSFSTKGATYITYVNFLNELRVKLKPEGNSHGIPLLRKKCDDPGKCFVLVALSNDNGQLAEIAIDVTSVYVVGYQVRNRSYFFKDAPDAAYEGLFKNTIKTRLHFGGSYPSLEGEKAYRETTDLGIEPLRIGIKKLDENAIDNYKPTEIASSLLVVIQMVSEAARFTFIENQIRNNFQQRIRPANNTISLENKWGKLSFQIRTSGANGMFSEAVELERANGKKYYVTAVDQVKPKIALLKFVDKDPK 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with RIPG_SURMU | P33186 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:251
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 
           RIPG_SURMU    47 GLDTVSFSTKGATYITYVNFLNELRVKLKPEGNSHGIPLLRKKCDDPGKCFVLVALSNDNGQLAEIAIDVTSVYVVGYQVRNRSYFFKDAPDAAYEGLFKNTIKTRLHFGGSYPSLEGEKAYRETTDLGIEPLRIGIKKLDENAIDNYKPTEIASSLLVVIQMVSEAARFTFIENQIRNNFQQRIRPANNTISLENKWGKLSFQIRTSGANGMFSEAVELERANGKKYYVTAVDQVKPKIALLKFVDKDPK 297
               SCOP domains d3ktzb_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 3ktzB01 B:1-168 Ricin (A subunit), domain 1                                                                                                                             3ktzB02 B:169-251 Ricin (A Subunit), domain 2                                       CATH domains
           Pfam domains (1) -----RIP-3ktzB01 B:6-208                                                                                                                                                                                        ------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----RIP-3ktzB02 B:6-208                                                                                                                                                                                        ------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh....ee..ee............eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhh....eeee.....hhhhhhh...hhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeehhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ktz B   1 GLDTVSFSTKGATYITYVNFLNELRVKLKPEGNSHGIPLLRKKCDDPGKCFVLVALSNDNGQLAEIAIDVTSVYVVGYQVRNRSYFFKDAPDAAYEGLFKNTIKTRLHFGGSYPSLEGEKAYRETTDLGIEPLRIGIKKLDENAIDNYKPTEIASSLLVVIQMVSEAARFTFIENQIRNNFQQRIRPANNTISLENKWGKLSFQIRTSGANGMFSEAVELERANGKKYYVTAVDQVKPKIALLKFVDKDPK 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: RIP] (62)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RIPG_SURMU | P33186)
molecular function
    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:0030598    rRNA N-glycosylase activity    Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RIPG_SURMU | P33186: 3ku0

(-) Related Entries Specified in the PDB File

3ku0