Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF FUCOSYLTRANSFERASE NODZ FROM BRADYRHIZOBIUM
 
Authors :  K. Brzezinski, T. Stepkowski, S. Panjikar, G. Bujacz, M. Jaskolski
Date :  28 Jun 06  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
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
    Synonym: NODZ

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:86 , ARG A:87 , TRP A:88 , ARG A:91 , GLN A:103 , ARG A:106 , GLU A:110BINDING SITE FOR RESIDUE PO4 A 1001
2AC2SOFTWAREPHE A:6 , SER A:79 , TRS A:2001 , HOH A:2004 , HOH A:2005BINDING SITE FOR RESIDUE PO4 A 1002
3AC3SOFTWAREGLU A:59 , ARG A:151 , SER A:152 , GLU A:153 , HOH A:2254BINDING SITE FOR RESIDUE PO4 A 1003
4AC4SOFTWARELYS A:3 , GLU A:4 , PHE A:6 , ILE A:70 , LEU A:78 , PO4 A:1002 , HOH A:2133 , HOH A:2144 , HOH A:2262BINDING SITE FOR RESIDUE TRS A 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:82 -Pro A:83
2Phe A:85 -Pro A:86
3Phe A:283 -Pro A:284
4Asn A:316 -Pro A:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HHC)

(-) 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:291
 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee.............hhhhhh....ee..eeee.hhhhhh......eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeee..------------hhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhh..ee....-----------hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh.eeeee.--....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hhc A   2 TKERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRH------------WADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPK-----------SAEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFD--NPGHLTMIDNP 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      
                                                                                                                                                                                                          178          191                                                  244         256                                             304  |          
                                                                                                                                                                                                                                                                                                                                           307
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HHC)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:316 - Pro A:317   [ RasMol ]  
    Gly A:82 - Pro A:83   [ RasMol ]  
    Phe A:283 - Pro A:284   [ RasMol ]  
    Phe A:85 - Pro A:86   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2hhc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9AQ17_BRASW | Q9AQ17
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.4.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9AQ17_BRASW | Q9AQ17
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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