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(-) Description

Title :  BINDING OF KINETIN IN THE ACTIVE SITE OF MISTLETOE LECTIN I
 
Authors :  P. H. Malecki, A. Meyer, W. Rypniewski, M. Szymanski, J. Barciszewski,
Date :  28 Jul 10  (Deposition) - 14 Sep 11  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Microgravity, Cytokinin, Active Site, Viscum Album, Ribosome Inactivating Proteins, Kinetin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. H. Malecki, W. Rypniewski, M. Szymanski, J. Barciszewski, A. Meyer
Binding Of The Plant Hormone Kinetin In The Active Site Of Mistletoe Lectin I From Viscum Album.
Biochim. Biophys. Acta V. 1824 334 2012
PubMed-ID: 22064121  |  Reference-DOI: 10.1016/J.BBAPAP.2011.10.013

(-) Compounds

Molecule 1 - BETA-GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN A ISOFORM 1
    Chains: A
    EC Number: 3.2.2.22
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Synonym: BETA-GALACTOSIDE-SPECIFIC LECTIN I, VISCUMIN, BETA- GALACTOSIDE-SPECIFIC LECTIN I CHAIN A ISOFORM 1, ML-I A, MLA, RRNA N- GLYCOSIDASE
    Tissue: SEMIPARASITIC PLANT
 
Molecule 2 - BETA-GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN B
    Chains: B
    EC Number: 3.2.2.22
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Synonym: BETA-GALACTOSIDE-SPECIFIC LECTIN I, VISCUMIN, BETA- GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN B, BETA-GALACTOSIDE-SPECIFIC LECTIN I CHAIN B, ML-I B, MLB
    Tissue: SEMIPARASITIC PLANT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2H351Ligand/IonN-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:115 , GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126BINDING SITE FOR RESIDUE SO4 A 500
02AC2SOFTWAREASP A:91 , ASN A:112 , HOH A:333 , HOH A:334BINDING SITE FOR RESIDUE NAG A 601
03AC3SOFTWARESER A:148 , THR A:149 , ARG A:150 , ASN B:352BINDING SITE FOR RESIDUE GOL A 801
04AC4SOFTWARETRP A:174 , ARG A:175 , GLN A:178 , HOH A:272 , HOH A:290BINDING SITE FOR RESIDUE GOL A 802
05AC5SOFTWARETYR A:76 , GLY A:113 , TYR A:115 , GLU A:119 , ARG A:125 , LEU A:157 , GLU A:165 , ARG A:168 , GLU A:196 , HOH A:298BINDING SITE FOR RESIDUE H35 A 255
06AC6SOFTWAREARG A:234 , ASP A:235 , HOH A:348 , HOH A:365 , GOL B:1 , LEU B:380 , ARG B:388 , TYR B:424BINDING SITE FOR RESIDUE GOL A 256
07AC7SOFTWAREGLY A:83 , ASP A:84 , ARG A:143 , HOH A:376BINDING SITE FOR RESIDUE GOL A 257
08AC8SOFTWAREHOH B:95 , HOH B:149 , ASN B:343 , LEU B:475 , HOH B:536 , NAG B:601BINDING SITE FOR RESIDUE NAG B 600
09AC9SOFTWAREHOH B:183 , TRP B:341 , NAG B:600BINDING SITE FOR RESIDUE NAG B 601
10BC1SOFTWAREPHE A:214 , PRO A:217 , THR B:258 , ASN B:291 , ASN B:383 , HOH B:523 , NAG B:603BINDING SITE FOR RESIDUE NAG B 602
11BC2SOFTWAREASN B:291 , LEU B:296 , NAG B:602 , NAG B:604BINDING SITE FOR RESIDUE NAG B 603
12BC3SOFTWARENAG B:603BINDING SITE FOR RESIDUE NAG B 604
13BC4SOFTWAREHOH B:5 , ASP B:274 , PHE B:276 , ASN B:308 , NAG B:607BINDING SITE FOR RESIDUE NAG B 606
14BC5SOFTWARENAG B:606BINDING SITE FOR RESIDUE NAG B 607
15BC6SOFTWAREASP B:270 , VAL B:271 , ASP B:273 , GLN B:283 , LYS B:288 , ASN B:294 , HOH B:548BINDING SITE FOR RESIDUE GOL B 800
16BC7SOFTWAREGLN A:134 , SER A:185 , HOH A:320 , HOH B:37 , MET B:324 , PHE B:326 , ALA B:331 , VAL B:332BINDING SITE FOR RESIDUE GOL B 803
17BC8SOFTWAREARG A:234 , GOL A:256 , HOH A:348 , HOH B:87 , HOH B:200 , TRP B:464 , VAL B:465 , PHE B:466BINDING SITE FOR RESIDUE GOL B 1
18BC9SOFTWAREPHE B:276 , HIS B:277 , ASP B:278BINDING SITE FOR RESIDUE GOL B 511

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:247 -B:252
2B:311 -B:328
3B:399 -B:412
4B:438 -B:455

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:115 -Pro A:116
2Ala A:223 -Pro A:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Asymmetric/Biological Unit (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_ML1_VISAL_001 *E48DML1_VISAL  ---  ---AA15D
02UniProtVAR_ML1_VISAL_002 *N145TML1_VISAL  ---  ---AN112T
03UniProtVAR_ML1_VISAL_003 *P149TML1_VISAL  ---  ---AP116T
04UniProtVAR_ML1_VISAL_004 *T173SML1_VISAL  ---  ---AT140S
05UniProtVAR_ML1_VISAL_005 *F177YML1_VISAL  ---  ---AF144Y
06UniProtVAR_ML1_VISAL_006 *T184AML1_VISAL  ---  ---AT151A
07UniProtVAR_ML1_VISAL_007 *Y212DML1_VISAL  ---  ---AY179D
08UniProtVAR_ML1_VISAL_008 *A217EML1_VISAL  ---  ---AA184E
09UniProtVAR_ML1_VISAL_009 *V223MML1_VISAL  ---  ---AV190M
10UniProtVAR_ML1_VISAL_010 *I251FML1_VISAL  ---  ---AI218F
11UniProtVAR_ML1_VISAL_011 *T264SML1_VISAL  ---  ---AT231S
12UniProtVAR_ML1_VISAL_012 *D268SML1_VISAL  ---  ---AD235S
13UniProtVAR_ML1_VISAL_013 *N319SML1_VISAL  ---  ---BN265S
14UniProtVAR_ML1_VISAL_014 *G357NML1_VISAL  ---  ---BG303N
15UniProtVAR_ML1_VISAL_015 *G458QML1_VISAL  ---  ---BG404Q
16UniProtVAR_ML1_VISAL_016 *C495VML1_VISAL  ---  ---BC441V
17UniProtVAR_ML1_VISAL_017 *G524YML1_VISAL  ---  ---BG470Y
18UniProtVAR_ML1_VISAL_018 *N531SML1_VISAL  ---  ---BN477S
19UniProtVAR_ML1_VISAL_019 *N531TML1_VISAL  ---  ---BN477T
   * 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:255-382
B:386-509

(-) Exons   (0, 0)

(no "Exon" information available for 3O5W)

(-) 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:248
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:248
                                    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 YERLRLRVTHQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNEGGDSITAAIDVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTDGVFNNPIRLAIPPGNFVTLTNVRDVIASLAIMLFVCG 281
               SCOP domains d3o5wa_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhh...ee..ee..............eeeeeee.....eeeeeee.....eeeeee..eeee................eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee...eeeeeeehhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------D------------------------------------------------------------------------------------------------T---T-----------------------S---Y------A---------------------------D----E-----M---------------------------F------------S---S------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o5w A   1 YERLRLRVTHQTTGAEYFSFITLLRDYVSSGSFSNNIPLLRQSTVPVSEGQRFVLVELTNAGGDSITAAIDVTNLYVVAYQAGDQSYFLSDAPAGAETHDFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIALAIAPGNIVTLTNVRDVIASLAIMLFVCG 248
                                    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:262
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:262
                                   312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562  
            ML1_VISAL   303 DVTCSASEPTVRIVGRNGMCVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVISQQNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGKPNQMWLPVP 564
               SCOP domains d3o5wb1 B:249-384 automated matches                                                                                                     d3o5wb2 B:385-510 automated matches                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhh..ee.....eee....eeee..........eee....hhhhh.ee......eeeeeeehhheeeeee..eeeee.....hhhh.eee.....eee.....eeee..........eeee.hhhhhhh.eee.....eee.....eeee.hhh.....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:255-382 UniProt: 309-436                                                                                 ---RICIN_B_LECTIN  PDB: B:386-509 UniProt: 440-563                                                                             - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o5w B 249 DVTCSASEPTVRIVGRNGMTVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKKDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVASQQNQRWALYGDGSIRPKQNQSQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPSLQRIIIYPATGKPNQMWLPVP 510
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508
   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  (0, 0)

(no "CATH Domain" information available for 3O5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O5W)

(-) 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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 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 2rg9 3d7w 4eb2 4jkx

(-) Related Entries Specified in the PDB File

1m2t MISTLETOE LECTIN I IN COMPLEX WITH ADENINE MONOPHOSPHATE
2r9k THE MISTLETOE LECTIN I--PHLORETAMIDE STRUCTURE REVEALS A NEW FUNCTION OF PLANT LECTINS
3d7w STRUCTURE OF MISTLETOE LECTIN I FROM VISCUM ALBUM IN COMPLEX WITH THE PHYTOHORMONE ZEATIN