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Title :   1.95 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF N-ACETYL-D-GLUCOSAMINE KINASE FROM VIBRIO VULNIFICUS.

Authors :   G. Minasov, Z. Wawrzak, O. Onopriyenko, T. Skarina, L. Papazisi, A. Sav W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)

Date :   13 Jan 12 (Deposition) - 25 Jan 12 (Release) - 25 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Minasov, Z. Wawrzak, O. Onopriyenko, T. Skarina, L. Papazisi, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 95 Angstrom Resolution Crystal Structure Of N-Acetyl-D-Glucosamine Kinase From Vibrio Vulnificus.
To Be Published
PubMed: search

Molecule 1 - N-ACETYL-D-GLUCOSAMINE KINASE
	Chains	:	A
	EC Number	:	2.7.1.59
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIPL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NAGK, VV1_2570
	Organism Scientific	:	VIBRIO VULNIFICUS
	Organism Taxid	:	672
	Strain	:	CMCP6
	Synonym	:	GLCNAC KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:157 , CYS A:177 , CYS A:179 , CYS A:184	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	ARG A:294	BINDING SITE FOR RESIDUE CL A 402
3	AC3	SOFTWARE	GLY A:254	BINDING SITE FOR RESIDUE CL A 403
4	AC4	SOFTWARE	ARG A:98 , SER A:99 , HOH A:561	BINDING SITE FOR RESIDUE SO4 A 404
5	AC5	SOFTWARE	PRO A:123 , VAL A:144 , PHE A:145 , SER A:146 , GLY A:147 , HIS A:247 , HOH A:563 , HOH A:582 , HOH A:634	BINDING SITE FOR RESIDUE GOL A 405

(no "SS Bond" information available for 4DB3)

(no "Cis Peptide Bond" information available for 4DB3)

(no "SAP(SNP)/Variant" information available for 4DB3)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	NAGK_VIBVU	130-157	1	A:130-157

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	NAGK_VIBVU	130-157	1	A:130-157

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	NAGK_VIBVU	130-157	2	A:130-157

(no "Exon" information available for 4DB3)

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:311
 aligned with NAGK_VIBVU | Q8D9M7 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:311
                                    1                                                                                                                                                                                                                                                                                                              
                                    |2        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 
           NAGK_VIBVU     - --------MYYGFDVGGTKIEFGAFNEKLERVATERVPTPTDDYPLLLETIAGLVAKYDQEFACEGKIGLGLPGMEDADDATVLTVNVPAAKGKPLRADLEAKIGRSVKIENDANCFALSEAWDEELQDAPSVMGLILGTGFGGGLIYEGKVFSGRNNVAGELGHMRLPLDAWFHLGDNAPLLGCGCGKKGCLDSYLSGRGFELLYAHYYGEEKKAIDIIKANAAGDEKAAEHVERFMELLAICFGNIFTANDPHVVALGGGLSNFELIYEEMPKRVPKYLLSVAKCPKIIKAKHGDSGGVRGAAFLNIKG 303
               SCOP domains d4db3a1 A:-7-117 automated matches                                                                                           d4db3a2 A:118-303 automated matches                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee...eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeee.eee......eee..hhhhh..hhhhhhhhhhh...eeeehhhhhhhhhhh........eeeeeee...eeeeeee..ee.........hhhhh..hhhhhhhh...............hhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------ROK  PDB: A:130-157         -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4db3 A  -7 NLYFQSNAMYYGFDVGGTKIEFGAFNEKLERVATERVPTPTDDYPLLLETIAGLVAKYDQEFACEGKIGLGLPGMEDADDATVLTVNVPAAKGKPLRADLEAKIGRSVKIENDANCFALSEAWDEELQDAPSVMGLILGTGFGGGLIYEGKVFSGRNNVAGELGHMRLPLDAWFHLGDNAPLLGCGCGKKGCLDSYLSGRGFELLYAHYYGEEKKAIDIIKANAAGDEKAAEHVERFMELLAICFGNIFTANDPHVVALGGGLSNFELIYEEMPKRVPKYLLSVAKCPKIIKAKHGDSGGVRGAAFLNIKG 303
                                     2        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

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: automated matches (111)

Protein domain: automated matches (111)

Vibrio vulnificus [TaxId: 672] (1)

1a	d4db3a1	A:-7-117
1b	d4db3a2	A:118-303

(no "CATH Domain" information available for 4DB3)

(no "Pfam Domain" information available for 4DB3)

Asymmetric Unit(hide GO term definitions)

Chain A (NAGK_VIBVU | Q8D9M7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0045127	N-acetylglucosamine kinase activity	Catalysis of the reaction: N-acetyl-D-glucosamine + ATP = N-acetyl-D-glucosamine 6-phosphate + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006044	N-acetylglucosamine metabolic process	The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	GO:0009254	peptidoglycan turnover	The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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Biological Units
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