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(-) Description

Title :  CRYSTAL STRUCTURE OF VISCUM ALBUM MISTLETOE LECTIN I IN NATIVE STATE AT 1.95 A RESOLUTION, COMPARISON OF STRUCTURE ACTIVE SITE CONFORMATION IN RICIN AND IN VISCUMIN
 
Authors :  N. U. Karpechenko, V. I. Timofeev, A. G. Gabdoulkhakov, A. M. Mikhailov
Date :  03 Oct 07  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribosome-Inactivating Protein Type Ii, Glycoprotein, Hydrolase, Lectin, Plant Defense, Protein Synthesis Inhibitor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. U. Karpechenko, V. I. Timofeev, A. G. Gabdoulkhakov, A. M. Mikhailo
Crystal Structure Of Viscum Album Mistletoe Lectin I In Native State At 1. 95 A Resolution, Comparison Of Structure Active Site Conformation In Ricin And In Viscumin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN A ISOFORM 1
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Synonym: BETA-GALACTOSIDE-SPECIFIC LECTIN I CHAIN A ISOFORM 1, MLA, ML-I A, RRNA N-GLYCOSIDASE
 
Molecule 2 - BETA-GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN B
    Chains: B
    Engineered: YES
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Synonym: BETA-GALACTOSIDE-SPECIFIC LECTIN I CHAIN B, MLB, ML-I B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
1AZI3Ligand/IonAZIDE ION
2CL2Ligand/IonCHLORIDE ION
3GOL15Ligand/IonGLYCEROL
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO41Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:90 , ASP A:91 , ASN A:112 , SER A:114 , HOH A:3213 , HOH A:3224 , HOH A:3271BINDING SITE FOR RESIDUE NAG A5003
02AC2SOFTWAREGLU A:119 , HIS A:124 , ARG A:125 , ASP A:126BINDING SITE FOR RESIDUE SO4 A4001
03AC3SOFTWAREASP A:211 , ASN A:232 , HOH A:3242 , ILE B:93 , LEU B:133 , ALA B:134BINDING SITE FOR RESIDUE AZI A4004
04AC4SOFTWAREGLN A:205 , HIS A:208 , ASN A:216BINDING SITE FOR RESIDUE CL A4021
05AC5SOFTWAREGLY A:123 , ARG A:150 , HOH A:3041BINDING SITE FOR RESIDUE CL A4022
06AC6SOFTWARETYR A:1 , ARG A:3 , LEU A:55 , HOH A:3055 , HOH A:3186BINDING SITE FOR RESIDUE GOL A4007
07AC7SOFTWARESER A:32 , ARG A:41 , GLN A:42BINDING SITE FOR RESIDUE GOL A4008
08AC8SOFTWAREGLY A:63 , ASP A:64 , SER A:65 , ARG A:143 , HOH A:3038 , HOH A:3039 , HOH A:3202 , GOL A:4019BINDING SITE FOR RESIDUE GOL A4009
09AC9SOFTWAREGLY A:95 , ALA A:96 , GLU A:97 , THR A:98BINDING SITE FOR RESIDUE GOL A4010
10BC1SOFTWAREARG A:175 , ASP A:189 , TYR A:191 , LEU A:222 , PRO B:263BINDING SITE FOR RESIDUE GOL A4011
11BC2SOFTWAREPRO A:171 , ARG A:175 , GLN A:178 , HOH A:3009 , ASP B:150BINDING SITE FOR RESIDUE GOL A4016
12BC3SOFTWAREGLN A:84 , ARG A:143 , HOH A:3201 , GOL A:4009BINDING SITE FOR RESIDUE GOL A4019
13BC4SOFTWARESER A:148 , THR A:149 , ARG A:150 , ASN B:105BINDING SITE FOR RESIDUE GOL A4020
14BC5SOFTWAREPRO A:217 , ILE B:11 , ASN B:44 , ASN B:136 , HOH B:3109 , HOH B:3132 , HOH B:3294BINDING SITE FOR RESIDUE NAG B5001
15BC6SOFTWAREASN B:96 , TYR B:126 , LEU B:228 , HOH B:3166 , HOH B:3318 , GOL B:4013BINDING SITE FOR RESIDUE NAG B5002
16BC7SOFTWAREASP B:27 , PHE B:29 , ASN B:61 , HOH B:3134 , HOH B:3136 , HOH B:3296BINDING SITE FOR RESIDUE NAG B5004
17BC8SOFTWAREGLN B:30 , ASP B:31 , HOH B:3135BINDING SITE FOR RESIDUE AZI B4003
18BC9SOFTWAREVAL B:218 , PHE B:219 , HOH B:3144 , HOH B:3145 , HOH B:3146BINDING SITE FOR RESIDUE AZI B4005
19CC1SOFTWAREASP B:235 , GLN B:238 , TYR B:249 , ASN B:256 , HOH B:3152BINDING SITE FOR RESIDUE GOL B4006
20CC2SOFTWAREASP B:23 , VAL B:24 , ARG B:25 , ASP B:26 , GLN B:36 , TRP B:38 , LYS B:41 , ASN B:47 , HOH B:3101 , HOH B:3238BINDING SITE FOR RESIDUE GOL B4012
21CC3SOFTWARELEU B:228 , HOH B:3228 , NAG B:5002BINDING SITE FOR RESIDUE GOL B4013
22CC4SOFTWAREARG A:154 , TYR B:68 , ALA B:72 , GLN B:122 , THR B:123 , HOH B:3097 , HOH B:3173 , HOH B:3178BINDING SITE FOR RESIDUE GOL B4014
23CC5SOFTWAREPRO A:129 , GLN A:134 , PHE B:79 , ALA B:84 , VAL B:85 , HOH B:3143 , HOH B:3174BINDING SITE FOR RESIDUE GOL B4015
24CC6SOFTWAREARG B:59 , ASN B:82 , HOH B:3316BINDING SITE FOR RESIDUE GOL B4017
25CC7SOFTWAREARG A:234 , ASP A:235 , HOH A:3022 , HOH A:3085 , ARG B:141 , LEU B:176 , PRO B:261 , HOH B:3021 , HOH B:3052 , HOH B:3144BINDING SITE FOR RESIDUE GOL B4018

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1B:64 -B:81
2B:152 -B:165
3B:191 -B:208

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RG9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Asymmetric/Biological Unit (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_ML1_VISAL_001 *E48DML1_VISAL  ---  ---AE15D
02UniProtVAR_ML1_VISAL_013 *N319SML1_VISAL  ---  ---BN18S
03UniProtVAR_ML1_VISAL_014 *G357NML1_VISAL  ---  ---BG56N
04UniProtVAR_ML1_VISAL_002 *N145TML1_VISAL  ---  ---AN112T
05UniProtVAR_ML1_VISAL_003 *P149TML1_VISAL  ---  ---AP116T
06UniProtVAR_ML1_VISAL_004 *T173SML1_VISAL  ---  ---AT140S
07UniProtVAR_ML1_VISAL_005 *F177YML1_VISAL  ---  ---AF144Y
08UniProtVAR_ML1_VISAL_006 *T184AML1_VISAL  ---  ---AT151A
09UniProtVAR_ML1_VISAL_015 *G458QML1_VISAL  ---  ---BG157Q
10UniProtVAR_ML1_VISAL_007 *Y212DML1_VISAL  ---  ---AY179D
11UniProtVAR_ML1_VISAL_008 *A217EML1_VISAL  ---  ---AA184E
12UniProtVAR_ML1_VISAL_009 *V223MML1_VISAL  ---  ---AV190M
13UniProtVAR_ML1_VISAL_016 *C495VML1_VISAL  ---  ---BN194V
14UniProtVAR_ML1_VISAL_010 *I251FML1_VISAL  ---  ---AI218F
15UniProtVAR_ML1_VISAL_017 *G524YML1_VISAL  ---  ---BG223Y
16UniProtVAR_ML1_VISAL_018 *N531SML1_VISAL  ---  ---BN230S
17UniProtVAR_ML1_VISAL_019 *N531TML1_VISAL  ---  ---BN230T
18UniProtVAR_ML1_VISAL_011 *T264SML1_VISAL  ---  ---AT231S
19UniProtVAR_ML1_VISAL_012 *D268SML1_VISAL  ---  ---AD235S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.ML1_VISAL309-436
440-563		  2B:8-135
B:139-262

(-) Exons   (0, 0)

(no "Exon" information available for 2RG9)

(-) 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:249
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:249
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273         
            ML1_VISAL    34 YERLRLRVTHQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNEGGDSITAAIDVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTDGVFNNPIRLAIPPGNFVTLTNVRDVIASLAIMLFVCGE 282
               SCOP domains d2rg9a_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains 2rg9A01 A:1-167 Ricin (A subunit), domain 1                                                                                                                            2rg9A02 A:168-247 Ricin (A Subunit), domain 2                                   -- CATH domains
               Pfam domains -----RIP-2rg9A01 A:6-209                                                                                                                                                                                         ---------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhheeeeee..eeee............eeeeeeee....eeeeeee.....eeeeee..eeee................eeee.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...eeeeeee.hhh............. Sec.struct. author
                 SAPs(SNPs) --------------D------------------------------------------------------------------------------------------------T---T-----------------------S---Y------A---------------------------D----E-----M---------------------------F------------S---S-------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rg9 A   1 YERLSLRTVQQTTGEEYFSFITLLRDFVSSGSFSNNIPLLRQSTIPVSEASRFVLVELTNEGGDSITAAIDVTNLYVVAYQAGQQSYFLKDAPRGAETQDFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIRLALPPGNVVTLTNIRDVIASLAIMLFVCGE 249
                                    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:263
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:263
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561   
            ML1_VISAL   302 DDVTCSASEPTVRIVGRNGMCVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVISQQNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGKPNQMWLPVP 564
               SCOP domains d2rg9b1 B:1-137 automated matches                                                                                                        d2rg9b2 B:138-263 automated matches                                                                                            SCOP domains
               CATH domains -2rg9B01 B:2-139  [code=2.80.10.50, no name defined]                                                                                       2rg9B02 B:140-263  [code=2.80.10.50, no name defined]                                                                        CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2rg9B01 B:139-259                                                                                         ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2rg9B02 B:139-259                                                                                         ---- Pfam domains (2)
         Sec.struct. author ..........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeee..........eee....hhhhh.ee......eeeeeehhh.........eeeeee....hhh.eeee.....eee.....eeee..........eeee....hhhh.eee.....eee.....eeee.........eeee....hhhhh.eee. Sec.struct. author
             SAPs(SNPs) (1) -----------------S-------------------------------------N----------------------------------------------------------------------------------------------------Q------------------------------------V----------------------------Y------S--------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------- SAPs(SNPs) (2)
                    PROSITE -------RICIN_B_LECTIN  PDB: B:8-135 UniProt: 309-436                                                                                   ---RICIN_B_LECTIN  PDB: B:139-262 UniProt: 440-563                                                                             - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rg9 B   1 DDVTCSASEPIVRIVGRNGMTVDVRDDDFQDGNQIQLWPSKSNNDPNQLWTIKKDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCTIGQENQRWALYGDGSIRPKQNQSQCLTNGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGNPNQMWLPVP 263
                                    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  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)
(-)
Clan: no clan defined [family: RIP] (62)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ML1_VISAL | P81446)
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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  2rg9
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  ML1_VISAL | P81446
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 Related Entries

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

UniProtKB/Swiss-Prot
        ML1_VISAL | P81446: 1ce7 1m2t 1onk 1oql 1pum 1puu 1sz6 2mll 2r9k 3d7w 3o5w 4eb2 4jkx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RG9)