3EGJ - JenaLib

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Title :   N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM VIBRIO CHOLERAE.

Authors :   J. Osipiuk, N. Maltseva, J. Stam, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)

Date :   10 Sep 08 (Deposition) - 23 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   N-Acetylglucosamine-6-Phosphate Deacetylase, Carbohydrate Metabolism, Idp01616, Hydrolase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osipiuk, N. Maltseva, J. Stam, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of N-Acetylglucosamine-6-Phosphate Deacetylase From Vibrio Cholerae.
To Be Published
PubMed: search

Molecule 1 - N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NAGA, VC_0994
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666
	Strain	:	O1 BIOVAR ELTOR STR. N16961
	Synonym	:	GLCNAC 6-P DEACETYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NI	2	Ligand/Ion	NICKEL (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:128 , HIS A:140 , HIS A:192 , HIS A:213 , HOH B:405	BINDING SITE FOR RESIDUE NI A 401
2	AC2	SOFTWARE	GLU B:128 , HIS B:192 , HIS B:213 , HOH B:406	BINDING SITE FOR RESIDUE NI B 402
3	AC3	SOFTWARE	ARG A:224 , PHE B:215 , ASN B:216 , ALA B:217	BINDING SITE FOR RESIDUE SO4 A 403
4	AC4	SOFTWARE	ASN A:216 , ALA A:217 , ARG B:224	BINDING SITE FOR RESIDUE SO4 B 404

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

Asymmetric Unit

No.	Residues
1	Gly A:129	-	Pro A:130
2	Gly B:129	-	Pro B:130

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

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

(no "Exon" information available for 3EGJ)

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:379
 aligned with NAGA_VIBCH | O32445 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:379
                              1                                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368         
           NAGA_VIBCH     - --MYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQLNGCGGVMFNDEITAETIDTMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPNQSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEKLVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYAGIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDENGTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVFDRDFNVKATVVNGQYEQ 377
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3egjA01 A:-1-54,A:342-377 Urease, subunit C, domain 1   3egjA02 A:55-277,A:278-341 Metal-dependent hydrolases                                                                                                                                                                          3egjA02 A:55-277,A:278-341 Metal-dependent hydrolases           3egjA01 A:-1-54,A:342-377            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee....ee..eeeeee..eeeeeee.hhh.....eee....eeee.eeeeee............hhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhh......eeee....hhhhh...........hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh..ee..............hhhhhhhhh....eeee.......hhhhhhhhhhhhh..eee.............eeee..eeeeee..eeee...ee.....hhhhhhhhhhhh...hhhhhhhh.hhhhhhhhh...............eeee.....eeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3egj A  -1 NAMYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQLNGCGGVMFNDEITAETIDTMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPNQSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEKLVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYAGIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDENGTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVFDRDFNVKATVVNGQYEQ 377
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368

Chain B from PDB  Type:PROTEIN  Length:361
 aligned with NAGA_VIBCH | O32445 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:379
                              1                                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368         
           NAGA_VIBCH     - --MYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQLNGCGGVMFNDEITAETIDTMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPNQSLGLHLEGPYLNVMKKGIHSVDFIRPSDDTMIDTICANSDVIAKVTLAPENNKPEHIEKLVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYAGIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDENGTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVFDRDFNVKATVVNGQYEQ 377
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3egjB01 B:-1-54,B:342-377 Urease, subunit C, domain 1   3egjB02 B:55-277,B:278-341 Metal-dependent hydrolases                                                                                                                                                                          3egjB02 B:55-277,B:278-341 Metal-dependent hydrolases           3egjB01 B:-1-54,B:342-377            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....ee..eeeeee..eeeeeee.hhh.....eeeeeeeeeee.eeeeee.ee..ee.....hhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhh......eeee..------------------hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh..ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeee............eee....eeee....ee...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....eeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3egj B  -1 NAMYALTNCKIYTGNDVLVKHAVIINGDKIEAVCPIESLPSEMNVVDLNGANLSPGFIDLQLNGCGGVMFNDEITAETIDTMHKANLKSGCTSFLPTLITSSDENMRQAIAAAREYQAKYPNQSLGLHLEGP------------------DDTMIDTICANSDVIAKVTLAPENNKPEHIEKLVKAGIVVSIGHTNATYSEARKSFESGITFATHLFNAMTPMVGREPGVVGAIYDTPEVYAGIIADGFHVDYANIRIAHKIKGEKLVLVTDATAPAGAEMDYFIFVGKKVYYRDGKCVDENGTLGGSALTMIEAVQNTVEHVGIALDEALRMATLYPAKAIGVDEKLGRIKKGMIANLTVFDRDFNVKATVVNGQYEQ 377
                                     8        18        28        38        48        58        68        78        88        98       108       118       128 |       -         -|      158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368         
                                                                                                                                                             130                149

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 3EGJ)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Vibrio cholerae. Organism_taxid: 666. Strain: o1 biovar eltor str. N16961. (1)

1a	3egjA02	A:55-277,A:278-341
1b	3egjB02	B:55-277,B:278-341

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Urease, subunit C; domain 1 (95)

Homologous Superfamily: Urease, subunit C, domain 1 (95)

Vibrio cholerae. Organism_taxid: 666. Strain: o1 biovar eltor str. N16961. (1)

2a	3egjA01	A:-1-54,A:342-377
2b	3egjB01	B:-1-54,B:342-377

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAGA_VIBCH | O32445)

molecular function
	GO:0008448	N-acetylglucosamine-6-phosphate deacetylase activity	Catalysis of the reaction: N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006046	N-acetylglucosamine catabolic process	The chemical reactions and pathways resulting in the breakdown of 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: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:0019262	N-acetylneuraminate catabolic process	The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
	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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.

Asymmetric Unit
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	Cis Peptide Bonds
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	NAGA_VIBCH \| O32445	:	3iv8

1yrr	N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM ESCHERICHIA COLI K12 AT 2.0 A RESOLUTION
2vhl	N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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