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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM ESCHERICHIA COLI K12

Authors :   A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo, S. K. B York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   21 Jan 05 (Deposition) - 01 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Naga, Nysgxrc Target T2187, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Fedorov, E. V. Fedorov, D. F. Xiang, F. M. Raushel, S. C. Almo
Crystal Structure Of The N-Acetylglucosamine-6-Phosphate Deacetylase From Escherichia Coli
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 Taxid	:	562
	Gene	:	NAGA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	GLCNAC 6-P DEACETYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YMY)

(no "Site" information available for 1YMY)

(no "SS Bond" information available for 1YMY)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:132	-	Pro A:133
2	Gly B:132	-	Pro B:133

(no "SAP(SNP)/Variant" information available for 1YMY)

(no "PROSITE Motif" information available for 1YMY)

(no "Exon" information available for 1YMY)

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:376
 aligned with NAGA_ECOLI | P0AF18 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:382
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  
           NAGA_ECOLI     1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
               SCOP domains d1ymya1 A:1-53,A:351-382                             d1ymya2 A:54-350 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain                                                                                                                                                                                                                     d1ymya1 A:1-53,A:351-382         SCOP domains
               CATH domains 1ymyA01 A:1-54,A:345-382 Urease, subunit C, domain 1  1ymyA02 A:55-280,A:281-344 Metal-dependent hydrolases                                                                                                                                                                             1ymyA02 A:55-280,A:281-344 Metal-dependent hydrolases           1ymyA01 A:1-54,A:345-382               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....ee..eeeeee..eeeeeee........eeeeeeeeeeee.eeeeee.ee..ee........hhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhh......eeee.......------....hhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeee............eeee..eeeee....eee..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhh.........eeee.....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ymy A   1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLV------PNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       | -    |  150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  
                                                                                                                                                                   138    145

Chain B from PDB  Type:PROTEIN  Length:331
 aligned with NAGA_ECOLI | P0AF18 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:382
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  
           NAGA_ECOLI     1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
               SCOP domains d1ymyb1 B:1-53,B:351-382                             d1ymyb2 B:54-35     0 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic d               omain                                                                                                                                                                                                 d1ymyb1 B:1-53,B:351-382         SCOP domains
               CATH domains 1ymyB01 B:1-54,B:346-382 Urease, subunit C, domain 1  1ymyB02 B:55-3     45 Metal-dependent hydrolases                                                                                                                                                                                                                                                   1ymyB01 B:1-54,B:346-382              CATH domains
           Pfam domains (1) -------------------------------------------------Amidohydro_1-1ymyB0     1 B:50-364                                                                                                                                                                                                                                                                                         ------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Amidohydro_1-1ymyB0     2 B:50-364                                                                                                                                                                                                                                                                                         ------------------ Pfam domains (2)
         Sec.struct. author .eeeeeeeee....ee..eeeeee..eeeeeee........eeeeeeeeeeee.eeeeee........-----..hhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhh......eeee......---------------hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...ee..............hhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeee.....-------------------------------....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhh.........eeee.....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ymy B   1 MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQLNGCGGVQF-----AVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAKHPNQALGLHLEGPWLNL---------------AALVDFLCENADVITKVTLAPEMVPAEVISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATA-------------------------------GSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANLTAFTPDFKITKTIVNGNEVVTQ 382
                                    10        20        30        40        50        60       | -   |    80        90       100       110       120       130      |  -         -  |    160       170       180       190       200       210       220       230       240       250       260       270     |   -         -         -       310       320       330       340       350       360       370       380  
                                                                                              68    74                                                            137             153                                                                                                                        276                             308

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/Biological 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)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (3)

1a	1ymyA02	A:55-280,A:281-344
1b	1ymyB02	B:55-345

Class: Mainly Beta (13760)

Architecture: Roll (1513)

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

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

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (3)

2a	1ymyA01	A:1-54,A:345-382
2b	1ymyB01	B:1-54,B:346-382

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Escherichia coli (strain K12) (12)

1a	Amidohydro_1-1ymyB01	B:50-364
1b	Amidohydro_1-1ymyB02	B:50-364

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NAGA_ECOLI | P0AF18)

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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1ymy)

	Sites
(no "Sites" information available for 1ymy)

	Cis Peptide Bonds
		Gly A:132 - Pro A:133	[ RasMol ]
		Gly B:132 - Pro B:133	[ RasMol ]

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	NAGA_ECOLI \| P0AF18	:	1yrr 2p50 2p53

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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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