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(-) Description

Title :  CRYSTALLOGRAPHIC REFINEMENT OF RICIN TO 2.5 ANGSTROMS
 
Authors :  E. Rutenber, B. J. Katzin, W. Montfort, J. E. Villafranca, S. R. Ernst, E. J. Collins, D. Mlsna, A. F. Monzingo, M. P. Ready, J. D. Robertus
Date :  07 Sep 93  (Deposition) - 31 Jan 94  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Rutenber, B. J. Katzin, S. Ernst, E. J. Collins, D. Mlsna, M. P. Ready J. D. Robertus
Crystallographic Refinement Of Ricin To 2. 5 A.
Proteins V. 10 240 1991
PubMed-ID: 1881880  |  Reference-DOI: 10.1002/PROT.340100308
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RICIN (A CHAIN)
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Organism Common: CASTOR BEAN
    Organism Scientific: RICINUS COMMUNIS
    Organism Taxid: 3988
 
Molecule 2 - RICIN (B CHAIN)
    Chains: B
    EC Number: 3.2.2.22
    Engineered: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric/Biological Unit (6, 14)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2BMA2Ligand/IonBETA-D-MANNOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:160 , SER A:265 , TRP B:93 , ASN B:95 , TYR B:125 , HOH B:675BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 95 RESIDUES 270 TO 274
2AC2SOFTWAREPHE A:226 , PRO A:229 , TYR A:243 , ILE B:10 , ASN B:135BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 135 RESIDUES 280 TO 284
3AC3SOFTWAREASP B:22 , ASP B:25 , GLN B:35 , TRP B:37 , LYS B:40 , ASN B:46 , HOH B:681BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 264 TO 265
4AC4SOFTWAREASP B:234 , VAL B:235 , ARG B:236 , ALA B:237 , HIS B:251 , ASN B:255BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 267 TO 268

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:259 -B:4
2B:20 -B:39
3B:63 -B:80
4B:151 -B:164
5B:190 -B:207

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.RICI_RICCO207-223  1A:172-188
2RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.RICI_RICCO321-448
451-575		  2B:7-134
B:137-261

(-) Exons   (0, 0)

(no "Exon" information available for 2AAI)

(-) 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:267
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:267
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       
           RICI_RICCO    36 IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 302
               SCOP domains d2aaia_ A: Ricin A-chain                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2aaiA01 A:1-179 Ricin (A subunit), domain 1                                                                                                                                        2aaiA02 A:180-267 Ricin (A Subunit), domain 2                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...hhhhhhhhhhhhhhhhh.........................eeeeee...eeeeee........eeeee..eeeee...hhhhhhhhh.........eee....hhhhhhhhhh........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh............................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aai A   1 IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 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       


Chain B from PDB  Type:PROTEIN  Length:262
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:262
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574  
           RICI_RICCO   315 ADVCMDPEPIVRIVGRNGLCVDVRDGRFHNGNAIQLWPCKSNTDANQLWTLKRDNTIRSNGKCLTTYGYSPGVYVMIYDCNTAATDATRWQIWDNGTIINPRSSLVLAATSGNSGTTLTVQTNIYAVSQGWLPTNNTQPFVTTIVGLYGLCLQANSGQVWIEDCSSEKAEQQWALYADGSIRPQQNRDNCLTSDSNIRETVVKILSCGPASSGQRWMFKNDGTILNLYSGLVLDVRASDPSLKQIILYPLHGDPNQIWLPLF 576
               SCOP domains d2aaib1 B:1-135 Plant cytotoxin B-chain (lectin)                                                                                       d2aaib2 B:136-262 Plant cytotoxin B-chain (lectin)                                                                              SCOP domains
               CATH domains 2aaiB01 B:1-138  [code=2.80.10.50, no name defined]                                                                                       2aaiB02 B:139-262  [code=2.80.10.50, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh.....hhh................hhhhh...................................hhhhh.....................................hhhhh...............hhhhh......................................................................................hhhhhhh.........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RICIN_B_LECTIN  PDB: B:7-134 UniProt: 321-448                                                                                   --RICIN_B_LECTIN  PDB: B:137-261 UniProt: 451-575                                                                              - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aai B   1 ADVCMDPEPIVRIVGRNGLCVDVRDGRFHNGNAIQLWPCKSNTDANQLWTLKRDNTIRSNGKCLTTYGYSPGVYVMIYDCNTAATDATRWQIWDNGTIINPRSSLVLAATSGNSGTTLTVQTNIYAVSQGWLPTNNTQPFVTTIVGLYGLCLQANSGQVWIEDCSSEKAEQQWALYADGSIRPQQNRDNCLTSDSNIRETVVKILSCGPASSGQRWMFKNDGTILNLYSGLVLDVRASDPSLKQIILYPLHGDPNQIWLPLF 262
                                    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 2AAI)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RICI_RICCO | P02879)
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: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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0031640    killing of cells of other organism    Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
    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.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

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 Related Entries

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

UniProtKB/Swiss-Prot
        RICI_RICCO | P02879: 1br5 1br6 1ifs 1ift 1ifu 1il3 1il4 1il5 1il9 1j1m 1obs 1obt 1rtc 1uq4 1uq5 2p8n 2pjo 2r2x 2r3d 2vc3 2vc4 3bjg 3ej5 3hio 3lc9 3mk9 3px8 3px9 3rti 3rtj 3srp 4esi 4huo 4hup 4hv3 4hv7 4imv 4kuc 4lgp 4lgr 4lgs 4lhj 4lhq 4mx1 4mx5 4q2v 4z9k 5boz 5ddz 5e1h 5gu4 5j56 5j57 5sv3

(-) Related Entries Specified in the PDB File

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