3SIX - JenaLib

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Title :   CRYSTAL STRUCTURE OF NODZ ALPHA-1,6-FUCOSYLTRANSFERASE SOAKED WITH GDP-FUCOSE

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 :   2.35

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)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , TYR A:45 , HIS A:175 , ARG A:177 , CYS A:222 , SER A:266 , ALA A:267 , ASP A:270 , PHE A:289	BINDING SITE FOR RESIDUE GDP A 401
2	AC2	SOFTWARE	GLU A:59 , ARG A:151 , SER A:152 , GLU A:153	BINDING SITE FOR RESIDUE PO4 A 501
3	AC3	SOFTWARE	ARG A:142 , HOH A:334	BINDING SITE FOR RESIDUE CL A 601

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 3SIX)

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
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Chain A from PDB  Type:PROTEIN  Length:292
 aligned with Q9AQ17_BRASW | Q9AQ17 from UniProtKB/TrEMBL  Length:324

    Alignment length:315
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312     
         Q9AQ17_BRASW     3 KERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRHGNGEDIMEHAPYWADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPKRFQADRAGPLHSAEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFDLSNPGHLTMIDNP 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
                 3six A   3 KERFVISRRRTGFGDCLWSLASAWSYAQRTGRTLVIDWRGSCYVEQPFSNAFPAFFEPVEDIAGVPVICDDRVNQLSFPGPFFPRWWNRPSIDCINRPDEQIFRERDELTELFQAREDSEANTIVCDACLMWRCSEEAERLIFRNIKLRSEIRARIDALYEEHFSGHSIIGVHVRH-------------ADSELALHQVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGLFPDVFAVPKR----------SAEMGIEGGASALIDMYLLARCATVIRFPPTSAFTRYARLLVPRIIEFDLSNPGHLTMIDNP 317
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     |   -       192       202       212       222       232       242  |      -   |   262       272       282       292       302       312     
                                                                                                                                                                                                         178           192                                                  245        256

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 '\|'

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

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

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

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:82 - Pro A:83	[ RasMol ]
		Phe A:283 - Pro A:284	[ RasMol ]
		Phe A:85 - Pro A:86	[ RasMol ]

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

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	3six
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	Q9AQ17_BRASW \| Q9AQ17
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	2.4.1.-
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	Q9AQ17_BRASW \| Q9AQ17
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UniProtKB/TrEMBL
	Q9AQ17_BRASW \| Q9AQ17	:	2hhc 2hlh 2ocx 3siw

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
3siw	CRYSTAL STRUCTURE OF NODZ ALFA1,6-FUCOSYLTRANSFERASE CO- CRYSTALLIZED WITH GDP

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

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Cis Peptide Bonds (3, 3)

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Gene Ontology (5, 5)

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