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(-) Description

Title :  CRYSTAL STRUCTURE OF HIMALAYAN MISTLETOE RIP REVEALS THE PRESENCE OF A NATURAL INHIBITOR AND A NEW FUNCTIONALLY ACTIVE SUGAR-BINDING SITE
 
Authors :  V. Mishra, S. Bilgrami, R. S. Sharma, P. Kaur, S. Yadav, C. Betzel, C. R. B T. P. Singh
Date :  31 Dec 04  (Deposition) - 08 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Himalayan Mistletoe, Ribosome Inactivating Protein, Viscum Album, Natural Inhibitor, Sugar-Binding Site, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Mishra, S. Bilgrami, R. S. Sharma, P. Kaur, S. Yadav, R. Krauspenhaar, C. Betzel, W. Voelter, C. R. Babu, T. P. Singh
Crystal Structure Of Himalayan Mistletoe Ribosome-Inactivating Protein Reveals The Presence Of A Natural Inhibitor And A New Functionally Active Sugar-Binding Site.
J. Biol. Chem. V. 280 20712 2005
PubMed-ID: 15774467  |  Reference-DOI: 10.1074/JBC.M500735200

(-) Compounds

Molecule 1 - BETA-GALACTOSIDE-SPECIFIC LECTIN 4
    Chains: A
    EC Number: 3.2.2.22
    Fragment: RESIDUES 1-240
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Strain: HIMALAYAN V.ALBUM
    Synonym: RIBOSOME-INACTIVATING PROTEIN, MISTLETOE LECTIN
 
Molecule 2 - BETA-GALACTOSIDE-SPECIFIC LECTIN 4
    Chains: B
    EC Number: 3.2.2.22
    Fragment: RESIDUES 1-255
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Strain: HIMALAYAN V.ALBUM
    Synonym: RIBOSOME-INACTIVATING PROTEIN, MISTLETOE LECTIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2BMA1Ligand/IonBETA-D-MANNOSE
3GAL3Ligand/IonBETA-D-GALACTOSE
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
6P6C1Ligand/Ion2-AMINO-4-ISOPROPYL-PTERIDINE-6-CARBOXYLIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:107BINDING SITE FOR RESIDUE NAG A 1003
02AC2SOFTWARETYR A:75 , SER A:109 , TYR A:110 , ARG A:162 , TRP A:193 , GLY A:194 , HOH A:1015BINDING SITE FOR RESIDUE P6C A 1001
03AC3SOFTWARETRP B:90 , ASN B:92 , NAG B:257BINDING SITE FOR RESIDUE NAG B 256
04AC4SOFTWARENAG B:256BINDING SITE FOR RESIDUE NAG B 257
05AC5SOFTWAREPHE A:208 , PRO A:211 , THR B:7 , ASN B:40 , ASN B:132 , NAG B:259BINDING SITE FOR RESIDUE NAG B 258
06AC6SOFTWARENAG B:258 , MAN B:260BINDING SITE FOR RESIDUE NAG B 259
07AC7SOFTWARENAG B:259 , BMA B:261BINDING SITE FOR RESIDUE MAN B 260
08AC8SOFTWAREMAN B:260BINDING SITE FOR RESIDUE BMA B 261
09AC9SOFTWAREASP B:23 , PHE B:25 , ASN B:57 , NAG B:263BINDING SITE FOR RESIDUE NAG B 262
10BC1SOFTWARENAG B:262 , MAN B:264BINDING SITE FOR RESIDUE NAG B 263
11BC2SOFTWARENAG B:263BINDING SITE FOR RESIDUE MAN B 264
12BC3SOFTWAREGAL B:266 , HOH B:1036BINDING SITE FOR RESIDUE BGC B 265
13BC4SOFTWAREASP B:229 , VAL B:230 , TYR B:241 , ASN B:248 , BGC B:265BINDING SITE FOR RESIDUE GAL B 266
14BC5SOFTWAREASP B:19 , ARG B:21 , ASP B:22 , GLN B:32 , TRP B:34 , LYS B:37 , ASN B:43 , LYS B:111BINDING SITE FOR RESIDUE GAL B 1013
15BC6SOFTWAREHOH A:1017 , TYR B:64 , TYR B:71 , MET B:73 , GAL B:1015BINDING SITE FOR RESIDUE BGC B 1014
16BC7SOFTWARESER A:179 , THR B:62 , THR B:63 , MET B:73 , ALA B:80 , VAL B:81 , ALA B:84 , BGC B:1014BINDING SITE FOR RESIDUE GAL B 1015

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:240 -B:1
2B:60 -B:77
3B:148 -B:161
4B:186 -B:202

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YF8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YF8)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.ML4_VISAL269-396
400-519		  2B:4-131
B:135-254

(-) Exons   (0, 0)

(no "Exon" information available for 1YF8)

(-) 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:240
 aligned with ML4_VISAL | Q6ITZ3 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
            ML4_VISAL     1 YERLDLDVTSQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSGGGVEAARFVLVELTNEGGDSITAAIDVTNLYVVAYQAGSQSYFLSGPGTHLFTGTTRSSLPFNGSYPDLEQYAGHRKQIPLGIDQLIQSVTALRFPGNTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTEGVFNNPIRLAIPGNFVTLTNVRDVIASLAIMLFVC 240
               SCOP domains d1yf8a_ A: Mistletoe lectin I A-chain                                                                                                                                                                                                            SCOP domains
               CATH domains -1yf8A01 A:2-161 Ricin (A subunit), domain 1                                                                                                                     1yf8A02 A:162-240 Ricin (A Subunit), domain 2                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhhhheeeeee..eeee...........eeeeeee.....eeeeeee.....eeeee....eee.....................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeee........eeeehhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yf8 A   1 YERLDLDVTSQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSGGGVEAARFVLVELTNEGGDSITAAIDVTNLYVVAYQAGSQSYFLSGPGTHLFTGTTRSSLPFNGSYPDLEQYAGHRKQIPLGIDQLIQSVTALRFPGNTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTEGVFNNPIRLAIPGNFVTLTNVRDVIASLAIMLFVC 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with ML4_VISAL | Q6ITZ3 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:255
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     
            ML4_VISAL   266 CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLALAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESNGGSVWVETCVSQQNDRWALYGDGSIRPEQNQDQCLTSGRDSVAGINIVSCSGGSSGQRWVFTNEGAILNLKNGLAMDVANPGLGQIIIYPATGKPNQMWLPVP 520
               SCOP domains d1yf8b1 B:1-133 Plant cytotoxin B-chain (lectin)                                                                                     d1yf8b2 B:134-255 Plant cytotoxin B-chain (lectin)                                                                         SCOP domains
               CATH domains 1yf8B01 B:1-135  [code=2.80.10.50, no name defined]                                                                                    1yf8B02 B:136-255  [code=2.80.10.50, no name defined]                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.eee...eeeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeee..........eee....hhhh.eee......eeeeeee...eeeeee..eeeeee...hhh.eeee.....eee.....eeee.........eeee....hhhh.eee.....eee.....eeee.......eeee....hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RICIN_B_LECTIN  PDB: B:4-131 UniProt: 269-396                                                                                   ---RICIN_B_LECTIN  PDB: B:135-254 UniProt: 400-519                                                                         - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf8 B   1 CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLALAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESNGGSVWVETCVSQQNDRWALYGDGSIRPEQNQDQCLTSGRDSVAGINIVSCSGGSSGQRWVFTNEGAILNLKNGLAMDVANPGLGQIIIYPATGKPNQMWLPVP 255
                                    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  (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 1YF8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ML4_VISAL | Q6ITZ3)
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: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
        ML4_VISAL | Q6ITZ3: 1ce7 1pc8 1tfm 2mll

(-) Related Entries Specified in the PDB File

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