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(-) Description

Title :  CRYSTAL STRUCTURE OF SE-MET FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM
 
Authors :  K. Brzezinski, T. Stepkowski, S. Panjikar, G. Bujacz, M. Jaskolski
Date :  21 Dec 06  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyltransferase, Fucosyltransferase, Nodz, Nodulation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Brzezinski, T. Stepkowski, S. Panjikar, G. Bujacz, M. Jaskolski
High-Resolution Structure Of Nodz Fucosyltransferase Involved In The Biosynthesis Of The Nodulation Factor.
Acta Biochim. Pol. V. 54 537 2007
PubMed-ID: 17762900
(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: 562
    Expression System Vector Type: PLASMID
    Gene: NODZ
    Organism Scientific: BRADYRHIZOBIUM SP.
    Organism Taxid: 133505
    Strain: WM9

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2PO43Ligand/IonPHOSPHATE ION
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:86 , TRP A:88 , ARG A:91 , GLN A:103 , ARG A:106 , GLU A:110BINDING SITE FOR RESIDUE PO4 A 331
2AC2SOFTWAREPHE A:6 , SER A:79 , TRS A:334 , HOH A:378BINDING SITE FOR RESIDUE PO4 A 332
3AC3SOFTWAREGLU A:59 , ARG A:151 , SER A:152 , GLU A:153 , HOH A:434BINDING SITE FOR RESIDUE PO4 A 333
4AC4SOFTWARELYS A:3 , GLU A:4 , ARG A:74 , LEU A:78 , PO4 A:332 , HOH A:447 , HOH A:474BINDING SITE FOR RESIDUE TRS A 334

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OCX)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:82 -Pro A:83
2Phe A:85 -Pro A:86
3Phe A:283 -Pro A:284

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OCX)

(-) Exons   (0, 0)

(no "Exon" information available for 2OCX)

(-) 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:292
 aligned with Q9AQ17_BRASW | Q9AQ17 from UniProtKB/TrEMBL  Length:324

    Alignment length:316
                                    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 TKERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRHGNGEDIMEHAPYWADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPKRFQADRAGPLHSAEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFDLSNPGHLTMIDNP 317
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains NodZ-2ocxA01 A:2-317                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee.............hhhhhh....ee..eeee.hhhhhh......eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeee..------------hhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhh..ee....------------hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh.eeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ocx A   2 TKERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLmWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRH------------WADSELALHQVCmAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPK------------AEmGIEGGASALIDmYLLARCATVIRFPPTSAFTRYARLLVPRIIEFDLSNPGHLTmIDNP 317
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 |     141       151       161       171      |  -       191       201 |     211       221       231       241  |      -     | 261       271       281       291       301       311 |    
                                                                                                                                                             133-MSE                                      178          191         203-MSE                                  244          257 |         271-MSE                                   313-MSE
                                                                                                                                                                                                                                                                                           259-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2OCX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OCX)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: NodZ] (1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological 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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  Cis Peptide Bonds
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2hhc CRYSTAL STRUCTURE OF FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM
2hlh CRYSTAL STRUCTURE OF FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM