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(-) Description

Title :  CRYSTAL STRUCTURE OF ABRIN-A
 
Authors :  T. H. Tahirov, T. -H. Lu, Y. -C. Liaw, S. -C. Chu, J. -Y. Lin
Date :  11 Nov 94  (Deposition) - 07 Feb 95  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycosidase/Carbohydrate Complex, Lectin, Lectin (Agglutinin), Glycoprotein, Plant Seed Protein, Plant Toxin, Protein Synthesis Inhibitor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Tahirov, T. H. Lu, Y. C. Liaw, Y. L. Chen, J. Y. Lin
Crystal Structure Of Abrin-A At 2. 14 A.
J. Mol. Biol. V. 250 354 1995
PubMed-ID: 7608980  |  Reference-DOI: 10.1006/JMBI.1995.0382
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ABRIN-A
    Chains: A
    Engineered: YES
    Organism Common: INDIAN LICORICE
    Organism Scientific: ABRUS PRECATORIUS
    Organism Taxid: 3816
 
Molecule 2 - ABRIN-A
    Chains: B
    Engineered: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2BMA2Ligand/IonBETA-D-MANNOSE
3MAN3Ligand/IonALPHA-D-MANNOSE
4NDG3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5NGZ1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP B:98 , ASN B:100 , TYR B:130 , LEU B:232 , NGZ B:269CBINDING SITE FOR RESIDUE NDG B 268C
02AC2SOFTWARENDG B:268C , MAN B:270C , HOH B:287BINDING SITE FOR RESIDUE NGZ B 269C
03AC3SOFTWARENGZ B:269C , MAN B:271C , BMA B:272C , HOH B:358 , HOH B:368BINDING SITE FOR RESIDUE MAN B 270C
04AC4SOFTWAREASP B:27 , ASP B:30 , ASN B:31 , LYS B:45 , ASN B:51 , MAN B:270C , HOH B:321 , HOH B:358 , HOH B:382BINDING SITE FOR RESIDUE MAN B 271C
05AC5SOFTWAREASP B:30 , ASN B:31 , MAN B:270CBINDING SITE FOR RESIDUE BMA B 272C
06AC6SOFTWAREGLN A:216 , GLU B:13 , PRO B:14 , THR B:15 , ASN B:140 , NDG B:274D , HOH B:374BINDING SITE FOR RESIDUE NDG B 273D
07AC7SOFTWARELEU B:48 , LEU B:53 , ASN B:140 , NDG B:273D , BGC B:275D , BMA B:277DBINDING SITE FOR RESIDUE NDG B 274D
08AC8SOFTWARELEU B:48 , NDG B:274D , MAN B:276D , BMA B:277DBINDING SITE FOR RESIDUE BGC B 275D
09AC9SOFTWAREARG B:47 , LEU B:48 , GLU B:49 , BGC B:275D , BMA B:277D , HOH B:359BINDING SITE FOR RESIDUE MAN B 276D
10ACTUNKNOWNTYR A:74 , TYR A:113 , GLU A:164 , ARG A:167 , TRP A:198 , ASN A:72 , ARG A:124 , GLN A:160 , GLU A:195 , ASN A:196ACTIVE SITE CLEFT OF ABRIN-A A-CHAIN CONTAINS 5 INVARIANT AND 5 CONSERVED RESIDUES. THE FIRST 5 RESIDUES IN THE LIST ARE INVARIANT RESIDUES.
11BC1SOFTWARELEU B:48 , NDG B:274D , BGC B:275D , MAN B:276DBINDING SITE FOR RESIDUE BMA B 277D
12GL1UNKNOWNASN B:100 , TYR B:130THE FIRST GLYCOSYLATION SITE OF ABRIN-A B- CHAIN BINDS N-ACETYLGLYCOSAMINE, NDG1, OF FIRST SUGAR CHAIN PRESENTED WITH INSERTION CODE C.
13GL2UNKNOWNASN B:140THE SECOND GLYCOSYLATION SITE OF ABRIN-A B- CHAIN BINDS N-ACETYLGLYCOSAMINES, NDG1 AND NDG2, OF THE SECOND SUGAR CHAIN PRESENTED WITH INSERTION CODE D.
14SU1UNKNOWNASN B:31 , ASN B:51THE FIRST SUGAR BINDING SITE OF ABRIN-A B- CHAIN BINDS MANNOSE, MAN4, OF THE SUGAR CHAIN WHICH SYMMETRICALLY RELATED TO THE FIRST SUGAR CHAIN IDENTIFIED WITH INSERTION CODE C.
15SU2UNKNOWNASN B:260THE POTENTIAL SECOND SUGAR BINDING SITE OF ABRIN-A B-CHAIN. THIS IS NOT CONFIRMED BY CURRENT STRUCTURE.

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:247 -B:8
2B:25 -B:44
3B:68 -B:85
4B:156 -B:169
5B:195 -B:212

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ABR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.ABRA_ABRPR159-175  1A:159-175
2RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.ABRA_ABRPR273-400
403-527		  2B:12-139
B:142-266

(-) Exons   (0, 0)

(no "Exon" information available for 1ABR)

(-) Sequences/Alignments

Asymmetric/Biological 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 ABRA_ABRPR | P11140 from UniProtKB/Swiss-Prot  Length:528

    Alignment length: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 
           ABRA_ABRPR     1 QDRPIKFSTEGATSQSYKQFIEALRERLRGGLIHDIPVLPDPTTLQERNRYITVELSNSDTESIEVGIDVTNAYVVAYRAGTQSYFLRDAPSSASDYLFTGTDQHSLPFYGTYGDLERWAHQSRQQIPLGLQALTHGISFFRSGGNDNEEKARTLIVIIQMVAEAARFRYISNRVRVSIQTGTAFQPDAAMISLENNWDNLSRGVQESVQDTFPNQVTLTNIRNEPVIVDSLSHPTVAVLALMLFVCNPPN 251
               SCOP domains d1abra_ A: Abrin A-chain                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1abrA01 A:1-166 Ricin (A subunit), domain 1                                                                                                                           1abrA02 A:167-251 Ricin (A Subunit), domain 2                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhhhhh..ee..ee........hhhh.eeeeeee.....eeeeeee.....eeeee...eeee......hhhhhh....eeee.......hhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1abr A   1 EDRPIKFSTEGATSQSYKQFIEALRERLRGGLIHDIPVLPDPTTLQERNRYITVELSNSDTESIEVGIDVTNAYVVAYRAGTQSYFLRDAPSSASDYLFTGTDQHSLPFYGTYGDLERWAHQSRQQIPLGLQALTHGISFFRSGGNDNEEKARTLIVIIQMVAEAARFRYISNRVRVSIQTGTAFQPDAAMISLENNWDNLSRGVQESVQDTFPNQVTLTNIRNEPVIVDSLSHPTVAVLALMLFVCNPPN 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:267
 aligned with ABRA_ABRPR | P11140 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:267
                                   271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
           ABRA_ABRPR   262 IVEKSKICSSRYEPTVRIGGRDGMCVDVYDNGYHNGNRIIMWKCKDRLEENQLWTLKSDKTIRSNGKCLTTYGYAPGSYVMIYDCTSAVAEATYWEIWDNGTIINPKSALVLSAESSSMGGTLTVQTNEYLMRQGWRTGNNTSPFVTSISGYSDLCMQAQGSNVWMADCDSNKKEQQWALYTDGSIRSVQNTNNCLTSKDHKQGSTILLMGCSNGWASQRWVFKNDGSIYSLYDDMVMDVKGSDPSLKQIILWPYTGKPNQIWLTLF 528
               SCOP domains d1abrb1 B:1-140 Plant cytotoxin B-chain (lectin)                                                                                            d1abrb2 B:141-267 Plant cytotoxin B-chain (lectin)                                                                              SCOP domains
               CATH domains ----1abrB01 B:5-143  [code=2.80.10.50, no name defined]                                                                                        1abrB02 B:144-267  [code=2.80.10.50, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhh..ee.....eee....eeee..........eee....hhhhh.ee......eee.eehhhhheeeee..eeeee.....hhhh.eee.....eee..eeeeeeee........eeeee....hhhhh.ee.....eee....eeeee.hhhhhhh.eeee....hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------RICIN_B_LECTIN  PDB: B:12-139 UniProt: 273-400                                                                                  --RICIN_B_LECTIN  PDB: B:142-266 UniProt: 403-527                                                                              - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1abr B   1 IVEKSKICSSRYEPTVRIGGRDGMCVDVYDNGYHNGNRIIMWKCKDRLEENQLWTLKSDKTIRSNGKCLTTYGYAPGSYVMIYDCTSAVAEATYWEIWDNGTIINPKSALVLSAESSSMGGTLTVQTNEYLMRQGWRTGNNTSPFVTSISGYSDLCMQAQGSNVWMADCDSNKKEQQWALYTDGSIRSVQNTNNCLTSKDHKQGSTILLMGCSNGWASQRWVFKNDGSIYSLYDDMVMDVKGSDPSLKQIILWPYTGKPNQIWLTLF 267
                                    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       260
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ABRA_ABRPR | P11140)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005534    galactose binding    Interacting selectively and non-covalently with the aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides.
    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.
    GO:0045807    positive regulation of endocytosis    Any process that activates or increases the frequency, rate or extent of endocytosis.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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  1abr
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