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(-) Description

Title :  CRYSTAL STRUCTURE OF NODZ ALPHA-1,6-FUCOSYLTRANSFERASE CO-CRYSTALLIZED WITH GDP
 
Authors :  K. Brzezinski, Z. Dauter, M. Jaskolski
Date :  20 Jun 11  (Deposition) - 08 Feb 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Family Gt23 Glycosyltransferase, Gt-B Fold, Alfa1, 6- Fucosyltransferase, Nodulation Protein, Chitooligosaccharide Fucosylation, Nod Factor Biosynthesis, Nitrogen Fixation, Legume- Rhizobium Symbiosis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Brzezinski, Z. Dauter, M. Jaskolski
Structures Of Nodz Alpha-1, 6-Fucosyltransferase In Complex With Gdp And Gdp-Fucose
Acta Crystallogr. , Sect. D V. 68 160 2012
PubMed-ID: 22281745  |  Reference-DOI: 10.1107/S0907444911053157
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NODULATION FUCOSYLTRANSFERASE NODZ
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NODZ
    Organism Scientific: BRADYRHIZOBIUM SP.
    Organism Taxid: 133505
    Strain: WM9
    Synonym: NODZ ALFA1,6-FUCOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2PO46Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , PHE A:15 , GLY A:16 , ASP A:17 , TYR A:45 , HIS A:175 , ARG A:177 , CYS A:222 , THR A:223 , ASP A:224 , SER A:266 , ALA A:267 , ASP A:270 , SER A:287 , ALA A:288 , PHE A:289 , HOH A:350 , HOH A:392 , HOH A:434 , HOH A:461BINDING SITE FOR RESIDUE GDP A 400
2AC2SOFTWAREGLU A:59 , ARG A:151 , SER A:152 , GLU A:153BINDING SITE FOR RESIDUE PO4 A 501
3AC3SOFTWAREARG A:282 , ARG A:294 , GLU A:302 , ILE A:314 , HOH A:436BINDING SITE FOR RESIDUE PO4 A 502
4AC4SOFTWAREPRO A:86 , ARG A:87 , TRP A:88 , GLN A:103 , ARG A:106 , GLU A:110 , HOH A:510BINDING SITE FOR RESIDUE PO4 A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SIW)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:82 -Pro A:83
2Phe A:85 -Pro A:86
3Phe A:283 -Pro A:284
4Pro A:317 -Tyr A:318

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SIW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SIW)

(-) Exons   (0, 0)

(no "Exon" information available for 3SIW)

(-) Sequences/Alignments

Asymmetric 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:290
 aligned with Q9AQ17_BRASW | Q9AQ17 from UniProtKB/TrEMBL  Length:324

    Alignment length:317
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       
         Q9AQ17_BRASW     2 TKERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRHGNGEDIMEHAPYWADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPKRFQADRAGPLHSAEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFDLSNPGHLTMIDNPY 318
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee.............hhhhhh....ee..eeee.hhhhhh......eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeee..-------------hhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhh..ee....------------hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh.eeeee.--....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3siw A   2 TKERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRH-------------ADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPK------------AEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFD--NPGHLTMIDNPY 318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      |  -         -|      201       211       221       231       241  |      -     | 261       271       281       291       301  |  | 311       
                                                                                                                                                                                                          178           192                                                 244          257                                            304  |           
                                                                                                                                                                                                                                                                                                                                           307
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3SIW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9AQ17_BRASW | Q9AQ17)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009877    nodulation    The formation of nitrogen-fixing root nodules on plant roots.
    GO:0009312    oligosaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9AQ17_BRASW | Q9AQ17: 2hhc 2hlh 2ocx 3six

(-) Related Entries Specified in the PDB File

2de0 CRYSTAL STRUCTURE OF HUMAN ALPHA 1,6-FUCOSYLTRANSFERASE, FUT8
2hhc CRYSTAL STRUCTURE OF FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM
2hlh CRYSTAL STRUCTURE OF FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM
2nzw CRYSTAL STRUCTURE OF ALPHA1,3-FUCOSYLTRANSFERASE
2nzx CRYSTAL STRUCTURE OF ALPHA1,3-FUCOSYLTRANSFERASE WITH GDP
2nzy CRYSTAL STRUCTURE OF ALPHA1,3-FUCOSYLTRANSFERASE WITH GDP- FUCOSE
2ocx CRYSTAL STRUCTURE OF SE-MET FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM
3six CRYSTAL STRUCTURE OF NODZ ALFA1,6-FUCOSYLTRANSFERASE SOAKED WITH GDP-FUCOSE