1NY1 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF B. SUBTILIS POLYSACCHARIDE DEACETYLASE NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR127.

Authors :   F. Forouhar, W. Edstrom, J. Khan, L. Ma, Y. Chiang, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   11 Feb 03 (Deposition) - 18 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Structural Genomics, Polysaccharide Deac, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Forouhar, W. Edstrom, J. Khan, L. Ma, Y. Chiang, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of Polysaccharide Deacetylase (Pdaa_bacsu) From B. Subtilis (Pdaa_bacsu) Northeast Structural Genomics Research Consortium (Nesg) Target Sr127
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	PDAA
	Gene	:	PDAA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	TARGET SR127 PROTEIN

		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 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1NY1)

(no "SS Bond" information available for 1NY1)

(no "Cis Peptide Bond" information available for 1NY1)

(no "SAP(SNP)/Variant" information available for 1NY1)

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	A:66-247 B: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	A: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	- B:66-247

(no "Exon" information available for 1NY1)

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:235
 aligned with PDAA_BACSU | O34928 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:235
                                    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 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEM 258
               SCOP domains d1ny1a_ A: Probable polysaccharide deacetylase PdaA                                                                                                                                                                                         SCOP domains
               CATH domains 1ny1A00 A:24-257 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.....hhhhhhhhhhhhhhhhh.eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------NODB  PDB: A:66-247 UniProt: 66-247                                                                                                                                                   ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ny1 A  24 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRmSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHmIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLmFEKEm 258
                                    33        43        53        63        73        83        93       103       113|      123       133       143       153       163       173       183       193       203     | 213       223       233       243       253    |
                                                                                                                    114-MSE                                                                                        209-MSE                                     253-MSE|
                                                                                                                                                                                                                                                                    258-MSE

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with PDAA_BACSU | O34928 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:235
                                    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 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRMSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHMIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLMFEKEM 258
               SCOP domains d1ny1b_ B: Probable polysaccharide deacetylase PdaA                                                                                                                                                                                         SCOP domains
               CATH domains 1ny1B00 B:24-257 Glycoside hydrolase/deacetylase                                                                                                                                                                                          - CATH domains
           Pfam domains (1) ------------------------------------Polysacc_deac_1-1ny1B01 B:60-185                                                                                              ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Polysacc_deac_1-1ny1B02 B:60-185                                                                                              ------------------------------------------------------------------------- Pfam domains (2)
         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: B:66-247 UniProt: 66-247                                                                                                                                                   ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ny1 B  24 VPNEPINWGFKRSVNHQPPDAGKQLNSLIEKYDAFYLGNTKEKTIYLTFDNGYENGYTPKVLDVLKKHRVTGTFFVTGHFVKDQPQLIKRmSDEGHIIGNHSFHHPDLTTKTADQIQDELDSVNEEVYKITGKQDNLYLRPPRGVFSEYVLKETKRLGYQTVFWSVAFVDWKINNQKGKKYAYDHmIKQAHPGAIYLLHTVSRDNAEALDDAITDLKKQGYTFKSIDDLmFEKEm 258
                                    33        43        53        63        73        83        93       103       113|      123       133       143       153       163       173       183       193       203     | 213       223       233       243       253    |
                                                                                                                    114-MSE                                                                                        209-MSE                                     253-MSE|
                                                                                                                                                                                                                                                                    258-MSE

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Probable polysaccharide deacetylase PdaA (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1ny1a_	A:
1b	d1ny1b_	B:

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. (1)

1a	1ny1A00	A:24-257
1b	1ny1B00	B:24-257

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GH_CE (28)

Family: Polysacc_deac_1 (9)

Bacillus subtilis (4)

1a	Polysacc_deac_1-1ny1B01	B:60-185
1b	Polysacc_deac_1-1ny1B02	B:60-185

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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