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Title :   ESCHERICHIA COLI PGAB N-TERMINAL DOMAIN

Authors :   T. Nishiyama, H. Noguchi, H. Yoshida, S. -Y. Park, J. R. H. Tame

Date :   05 Jul 12 (Deposition) - 14 Nov 12 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Poly-Beta-1, 6-N-Acetyl-D-Glucosamine N-Deacetylase, Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nishiyama, H. Noguchi, H. Yoshida, S. Y. Park, J. R. Tame
The Structure Of The Deacetylase Domain Of Escherichia Coli Pgab, An Enzyme Required For Biofilm Formation: A Circularl Permuted Member Of The Carbohydrate Esterase 4 Family
Acta Crystallogr. , Sect. D V. 69 44 2013
PubMed-ID: 23275162 | Reference-DOI: 10.1107/S0907444912042059

Molecule 1 - POLY-BETA-1,6-N-ACETYL-D-GLUCOSAMINE N-DEACETYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DEACETYLASE DOMAIN, UNP RESIDUES 42-309
	Gene	:	B1023, JW5142, PGAB, YCDR
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PGA N-DEACETYLASE, POLY-BETA-1,6-GLCNAC N-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, 5)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	HG	1	Ligand/Ion	MERCURY (II) ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HG	-1	Ligand/Ion	MERCURY (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HG	-1	Ligand/Ion	MERCURY (II) ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:115 , HIS A:184 , HIS A:189 , ACT A:402	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	HIS A:55 , ASP A:114 , ASP A:115 , HIS A:184 , HIS A:189 , TRP A:250 , PRO A:251 , TYR A:252 , ARG A:289 , ZN A:401	BINDING SITE FOR RESIDUE ACT A 402
3	AC3	SOFTWARE	HIS B:55 , ASP B:115 , HIS B:184 , HIS B:189 , ACT B:402	BINDING SITE FOR RESIDUE ZN B 401
4	AC4	SOFTWARE	HIS B:55 , ASP B:114 , ASP B:115 , HIS B:184 , HIS B:189 , TRP B:250 , PRO B:251 , TYR B:252 , LEU B:274 , ARG B:289 , ZN B:401 , HOH B:584	BINDING SITE FOR RESIDUE ACT B 402
5	AC5	SOFTWARE	HIS B:98	BINDING SITE FOR RESIDUE HG B 403

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

(no "Cis Peptide Bond" information available for 3VUS)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NODB	PS51677	NodB homology domain profile.	PGAB_ECOLI	107-349	2	A:107-309 B:107-308

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NODB	PS51677	NodB homology domain profile.	PGAB_ECOLI	107-349	1	A:107-309 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NODB	PS51677	NodB homology domain profile.	PGAB_ECOLI	107-349	1	- B:107-308

(no "Exon" information available for 3VUS)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:263
 aligned with PGAB_ECOLI | P75906 from UniProtKB/Swiss-Prot  Length:672

    Alignment length:268
                                    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        
           PGAB_ECOLI    42 QPWPHNGFVAISWHNVEDEAADQRFMSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQANATGSLLPVYVNRAYFTDHARYETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITVQ 309
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee..ee....hhhhh.eehhhhhhhhhhhhhh..ee.hhhhhhhhhh........eeeeeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhh......eee..eeehhhhh.hhhhhhhhhhh..eee..............-----.hhhhh..ee....ee.hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh.hhhhhhhhhhh...eee......ee.........ee.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------NODB  PDB: A:107-309 UniProt: 107-349                                                                                                                                                                       PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vus A  42 QPWPHNGFVAISWHNVEDEAADQRFMSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQAN-----LPVYVNRAYFTDHARYETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITVQ 309
                                    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        
                                                                                                                                                                                   195   201

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with PGAB_ECOLI | P75906 from UniProtKB/Swiss-Prot  Length:672

    Alignment length:266
                                    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      
           PGAB_ECOLI    43 PWPHNGFVAISWHNVEDEAADQRFMSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQANATGSLLPVYVNRAYFTDHARYETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITV 308
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..ee.----.....eehhhhhhhhhhhhhh..ee.hhhhhhhhhh........eeeeeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhh......eee..eeehhhhh.hhhhhhhhhhh..eee.............------.hhhhh..ee....ee.hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh.hhhhhhhhhhh...eee......ee.........ee.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------NODB  PDB: B:107-308 UniProt: 107-349                                                                                                                                                                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vus B  43 PWPHNGFVAISWHNVED----QRFMSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQA------LPVYVNRAYFTDHARYETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITV 308
                                    52      |  - |      72        82        92       102       112       122       132       142       152       162       172       182       192 |     202       212       222       232       242       252       262       272       282       292       302      
                                           59   64                                                                                                                               194    201

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 3VUS)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGAB_ECOLI | P75906)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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.
biological process
	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:0098732	macromolecule deacylation	The removal of an acyl group, any group or radical of the form RCO- where R is an organic group, from a macromolecule.
	GO:0044010	single-species biofilm formation	A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0031246	intrinsic component of periplasmic side of cell outer membrane	The component of the cell outer membrane consisting of the gene products that that penetrate the periplasmic side of the cell outer membrane only, either directly or via some covalently attached hydrophobic anchor.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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Ligands, Modified Residues, Ions (3, 5)

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