1W1A - JenaLib

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Title :   STRUCTURE OF BACILLUS SUBTILIS PDAA IN COMPLEX WITH NAG, A FAMILY 4 CARBOHYDRATE ESTERASE.

Authors :   D. E. Blair, D. M. F. Van Aalten

Date :   18 Jun 04 (Deposition) - 10 Jan 05 (Release) - 20 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Family 4 Carbohydrate Esterase, Deacetylase, Peptidoglycan, Nodb Homology Domain, Hydrolase, Sporulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. E. Blair, D. M. F. Van Aalten
Structure Of Bacillus Subtilis Pdaa, A Family 4 Carbohydrate Esterase, And A Complex With N-Acetyl- Glucosamine
Febs Lett. V. 570 13 2004
PubMed-ID: 15251431 | Reference-DOI: 10.1016/J.FEBSLET.2004.06.013

Molecule 1 - PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
	Chains	:	1, 2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21DE3
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	PDAA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CD	2	Ligand/Ion	CADMIUM ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP 1:73 , GLY 1:75 , HIS 1:124 , HIS 1:128 , ARG 1:166 , LEU 1:220 , HIS 1:222 , GOL 1:1260 , HOH 1:2142	BINDING SITE FOR RESIDUE NDG 11261
2	AC2	SOFTWARE	ASP 2:73 , GLY 2:75 , HIS 2:124 , HIS 2:128 , PRO 2:165 , ARG 2:166 , LEU 2:220 , HIS 2:222 , GOL 2:1260 , HOH 2:2115 , HOH 2:2116	BINDING SITE FOR RESIDUE NDG 21261
3	AC3	SOFTWARE	HIS 1:127	BINDING SITE FOR RESIDUE CD 11259
4	AC4	SOFTWARE	HIS 2:127	BINDING SITE FOR RESIDUE CD 21259
5	AC5	SOFTWARE	TRP 1:194 , NDG 1:1261	BINDING SITE FOR RESIDUE GOL 11260
6	AC6	SOFTWARE	TRP 2:194 , NDG 2:1261 , HOH 2:2027	BINDING SITE FOR RESIDUE GOL 21260

(no "SS Bond" information available for 1W1A)

(no "Cis Peptide Bond" information available for 1W1A)

(no "SAP(SNP)/Variant" information available for 1W1A)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NODB	PS51677	NodB homology domain profile.	PDAA_BACSU	66-247	2	1:66-247 2:66-247

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NODB	PS51677	NodB homology domain profile.	PDAA_BACSU	66-247	1	1:66-247 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NODB	PS51677	NodB homology domain profile.	PDAA_BACSU	66-247	1	- 2:66-247

(no "Exon" information available for 1W1A)

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 1 from PDB  Type:PROTEIN  Length:236
 aligned with PDAA_BACSU | O34928 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:236
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
           PDAA_BACSU    24 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEMR 259
               SCOP domains d1w1a1_ 1: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 1w1a100 1:24-259 Glycoside hydrolase/deacetylase                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..............hhhhhhhhhhh...........eeeeeeee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhh.eehhhhhhhhhhh..ee..........hhhhh.hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh..eeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------NODB  PDB: 1:66-247 UniProt: 66-247                                                                                                                                                   ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w1a 1  24 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEMR 259
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

Chain 2 from PDB  Type:PROTEIN  Length:236
 aligned with PDAA_BACSU | O34928 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:236
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
           PDAA_BACSU    24 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEMR 259
               SCOP domains d1w1a2_ 2: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 1w1a200 2:24-259 Glycoside hydrolase/deacetylase                                                                                                                                                                                             CATH domains
           Pfam domains (1) ------------------------------------Polysacc_deac_1-1w1a201 2:60-185                                                                                              -------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Polysacc_deac_1-1w1a202 2:60-185                                                                                              -------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....ee.............hhhhhhhhhhhh...........eeeeeeee.....hhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhh.eehhhhhhhhhhh..ee..........hhhhh.hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh..eeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------NODB  PDB: 2:66-247 UniProt: 66-247                                                                                                                                                   ------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w1a 2  24 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEMR 259
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

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(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: 7-stranded beta/alpha barrel (137)

Superfamily: Glycoside hydrolase/deacetylase (89)

Family: NodB-like polysaccharide deacetylase (12)

Protein domain: automated matches (5)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1w1a1_	1:
1b	d1w1a2_	2:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycoside hydrolase/deacetylase (11)

Bacillus subtilis. Organism_taxid: 1423. (3)

1a	1w1a100	1:24-259
1b	1w1a200	2:24-259

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GH_CE (28)

Family: Polysacc_deac_1 (9)

Bacillus subtilis (4)

1a	Polysacc_deac_1-1w1a201	2:60-185
1b	Polysacc_deac_1-1w1a202	2:60-185

Asymmetric Unit(hide GO term definitions)

Chain 1,2 (PDAA_BACSU | O34928)

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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

Asymmetric Unit
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	1w1a
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	PDAA_BACSU \| O34928	:	1ny1 1w17 1w1b

1ny1	CRYSTAL STRUCTURE OF B. SUBTILIS POLYSACCHARIDE DEACETYLASENORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR127.
1w17	STRUCTURE OF BACILLUS SUBTILIS PDAA, A FAMILY 4 CARBOHYDRATE ESTERASE.
1w1b	STRUCTURE OF BACILLUS SUBTILIS PDAA, A FAMILY 4 CARBOHYDRATE ESTERASE.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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