2VHL - JenaLib

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Title :   THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS

Authors :   F. Vincent, D. Yates, E. Garman, G. J. Davies

Date :   22 Nov 07 (Deposition) - 04 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   N- Acetyleglucosamine-6-Phosphate, Carbohydrate Metabolism, Hydrolase, Deacetylase, Bacillus Subtilis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Vincent, D. Yates, E. Garman, G. J. Davies
The Three-Dimensional Structure Of The N- Acetylglucosamine-6-Phosphate Deacetylase From Bacillus Subtilis
J. Biol. Chem. V. 279 2809 2004
PubMed-ID: 14557261 | Reference-DOI: 10.1074/JBC.M310165200

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	:	PDEST14
	Expression System Strain	:	IG20
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Other Details	:	AUTHORS ACKNOWLEDGE DR. DAAN VAN AALTEN FOR FOR INDICATING ERROR IN THEIR PDB ENTRY 1UN7
	Synonym	:	GLCNAC 6-P DEACETYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION
2	GLP	2	Ligand/Ion	GLUCOSAMINE 6-PHOSPHATE
3	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	GLP	1	Ligand/Ion	GLUCOSAMINE 6-PHOSPHATE
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	GLP	1	Ligand/Ion	GLUCOSAMINE 6-PHOSPHATE
3	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:146 , ALA A:147 , HIS A:202 , ASN A:226 , ALA A:227 , HIS A:233 , ARG A:234 , HIS A:258 , ASP A:281 , THR A:313 , LEU A:314 , GLY A:316 , FE A:1398 , HOH A:2199 , HOH A:2318 , HOH A:2319 , HOH A:2320 , HOH A:2321 , HOH A:2322	BINDING SITE FOR RESIDUE GLP A1395
2	AC2	SOFTWARE	ASP A:246 , LYS A:265 , PHE A:331 , THR A:332 , ASN A:333	BINDING SITE FOR RESIDUE PGE A1396
3	AC3	SOFTWARE	HIS A:63 , HIS A:65 , GLU A:136 , ASP A:281 , FE A:1398 , HOH A:2321	BINDING SITE FOR RESIDUE FE A1397
4	AC4	SOFTWARE	GLU A:136 , HIS A:202 , HIS A:223 , GLP A:1395 , FE A:1397 , HOH A:2321	BINDING SITE FOR RESIDUE FE A1398
5	AC5	SOFTWARE	GLY B:146 , ALA B:147 , HIS B:202 , ASN B:226 , ALA B:227 , HIS B:233 , ARG B:234 , HIS B:258 , ASP B:281 , THR B:313 , LEU B:314 , GLY B:316 , FE B:1397 , HOH B:2127 , HOH B:2184 , HOH B:2224 , HOH B:2300 , HOH B:2301 , HOH B:2302	BINDING SITE FOR RESIDUE GLP B1395
6	AC6	SOFTWARE	HIS B:245 , ASP B:246 , LYS B:265 , PHE B:331 , THR B:332 , ASN B:333	BINDING SITE FOR RESIDUE PGE B1396
7	AC7	SOFTWARE	GLU B:136 , HIS B:202 , HIS B:223 , GLP B:1395 , FE B:1398 , HOH B:2224 , HOH B:2301	BINDING SITE FOR RESIDUE FE B1397
8	AC8	SOFTWARE	HIS B:63 , HIS B:65 , GLU B:136 , ASP B:281 , FE B:1397 , HOH B:2224	BINDING SITE FOR RESIDUE FE B1398

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

Asymmetric Unit

No.	Residues
1	Gly A:137	-	Pro A:138
2	Gly B:137	-	Pro B:138

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

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

(no "Exon" information available for 2VHL)

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:392
 aligned with NAGA_BACSU | O34450 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:392
                                    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       322       332       342       352       362       372       382       392  
           NAGA_BACSU     3 ESLLIKDIAIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKEIQAPADSVLLPGMIDIHIHGGYGADTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAEESSLLGAELLGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEEDQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGTALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVTVRGRTALLSDGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVTVGKDADLVIVSSDCEVILTICRGNIAFISKEAD 394
               SCOP domains d2vhla1 A:3-57,A:359-394                               d2vhla2 A:58-358 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                                         d2vhla1 A:3-57,A:359-394             SCOP domains
               CATH domains 2vhlA01 A:3-57,A:359-394 Urease, subunit C, domain 1   2vhlA02 A:58-358 Metal-dependent hydrolases                                                                                                                                                                                                                                                                  2vhlA01 A:3-57,A:359-394             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeeee..eeeeee.........eeee.....eeee.eeeeee.ee..ee.hhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhh...hhhhh...hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeee...........eeeee..eeeeee..eee...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...............eeee.....eeeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vhl A   3 ESLLIKDIAIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKEIQAPADSVLLPGMIDIHIHGGYGADTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAEESSLLGAELLGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEEDQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGTALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVTVRGRTALLSDGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVTVGKDADLVIVSSDCEVILTICRGNIAFISKEAD 394
                                    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       322       332       342       352       362       372       382       392

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with NAGA_BACSU | O34450 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:393
                                    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       321       331       341       351       361       371       381       391   
           NAGA_BACSU     2 AESLLIKDIAIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKEIQAPADSVLLPGMIDIHIHGGYGADTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAEESSLLGAELLGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEEDQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGTALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVTVRGRTALLSDGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVTVGKDADLVIVSSDCEVILTICRGNIAFISKEAD 394
               SCOP domains d2vhlb1 B:2-57,B:359-394                                d2vhlb2 B:58-358 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                                         d2vhlb1 B:2-57,B:359-394             SCOP domains
               CATH domains 2vhlB01 B:2-57,B:359-394 Urease, subunit C, domain 1    2vhlB02 B:58-358 Metal-dependent hydrolases                                                                                                                                                                                                                                                                  2vhlB01 B:2-57,B:359-394             CATH domains
           Pfam domains (1) ----------------------------------------------------Amidohydro_1-2vhlB01 B:54-372                                                                                                                                                                                                                                                                                                  ---------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------Amidohydro_1-2vhlB02 B:54-372                                                                                                                                                                                                                                                                                                  ---------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee....eeeeeeeeee..eeeeee.........eeee.....eeee.eeeeee.ee..ee.hhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhhhh.hhhhh..eeeeeeee....hhhhh...hhhhh...hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeee...........eeeee..eeeeee..eee...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eeee.....eeeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vhl B   2 AESLLIKDIAIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKEIQAPADSVLLPGMIDIHIHGGYGADTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAEESSLLGAELLGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEEDQHFELIRHLKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGTALAHDGFVTELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVTVRGRTALLSDGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVTVGKDADLVIVSSDCEVILTICRGNIAFISKEAD 394
                                    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       321       331       341       351       361       371       381       391

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Bacillus subtilis. Organism_taxid: 1423. (1)

1a	2vhlA02	A:58-358
1b	2vhlB02	B:58-358

Class: Mainly Beta (13760)

Architecture: Roll (1513)

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

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

Bacillus subtilis. Organism_taxid: 1423. (1)

2a	2vhlB01	B:2-57,B:359-394
2b	2vhlA01	A:3-57,A:359-394

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Bacillus subtilis (1)

1a	Amidohydro_1-2vhlB01	B:54-372
1b	Amidohydro_1-2vhlB02	B:54-372

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAGA_BACSU | O34450)

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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:137 - Pro A:138	[ RasMol ]
		Gly B:137 - Pro B:138	[ RasMol ]

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	2vhl
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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