2WAG - JenaLib

Title :   THE STRUCTURE OF A FAMILY 25 GLYCOSYL HYDROLASE FROM BACILLUS ANTHRACIS.

Authors :   C. Martinez-Fleites, J. E. Korczynska, M. Cope, J. P. Turkenburg, E. J. Taylor

Date :   06 Feb 09 (Deposition) - 23 Jun 09 (Release) - 08 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Hydrolase, Gh25, Lysin, Lysozyme, Bacillus Anthracis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Martinez-Fleites, J. E. Korczynska, M. Cope, J. P. Turkenburg, E. J. Taylor
The Crystal Structure Of A Family Gh25 Lysozyme From Bacillus Anthracis Implies A Neighboring-Group Catalytic Mechanism With Retention Of Anomeric Configuration
Carbohydr. Res. V. 344 1753 2009
PubMed-ID: 19595298 | Reference-DOI: 10.1016/J.CARRES.2009.06.001

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:2 , SER A:3 , ASN A:187 , ARG A:188 , TYR A:200 , HOH A:2004 , HOH A:2349 , HOH A:2351 , HOH A:2352 , HOH A:2353	BINDING SITE FOR RESIDUE SO4 A1219
02	AC2	SOFTWARE	HIS A:9 , HIS A:10 , TYR A:185 , LYS A:190 , HOH A:2043 , HOH A:2354 , HOH A:2355	BINDING SITE FOR RESIDUE SO4 A1220
03	AC3	SOFTWARE	MET A:11 , ASP A:12 , ARG A:13	BINDING SITE FOR RESIDUE SO4 A1221
04	AC4	SOFTWARE	ARG A:166 , SER A:167 , VAL A:168 , HOH A:2285 , HOH A:2357 , HOH A:2358 , HOH A:2359 , HOH A:2360 , HOH A:2361	BINDING SITE FOR RESIDUE SO4 A1222
05	AC5	SOFTWARE	GLY A:48 , SER A:49 , SER A:77 , ASP A:79 , SER A:80 , HOH A:2101 , HOH A:2159 , HOH A:2362 , HOH A:2363 , HOH A:2364 , HOH A:2365 , HOH A:2366	BINDING SITE FOR RESIDUE SO4 A1223
06	AC6	SOFTWARE	ILE A:28 , ASP A:29 , GLU A:32 , LEU A:33 , GLN A:36 , LEU A:191 , HOH A:2318 , HOH A:2367 , HOH A:2368 , HOH A:2369	BINDING SITE FOR RESIDUE GOL A1224
07	AC7	SOFTWARE	LYS A:179 , THR A:181 , TYR A:207 , 15P A:1229 , 15P A:1230 , HOH A:2280	BINDING SITE FOR RESIDUE GOL A1225
08	AC8	SOFTWARE	PHE A:78 , ASP A:79 , SER A:80 , LYS A:81 , ASP A:121 , HOH A:2370	BINDING SITE FOR RESIDUE 15P A1226
09	AC9	SOFTWARE	ILE A:90 , ARG A:91 , ASN A:92 , PRO A:94 , HOH A:2169	BINDING SITE FOR RESIDUE 15P A1227
10	BC1	SOFTWARE	GLU A:83 , LYS A:118 , ARG A:119 , GLU A:120 , HOH A:2212	BINDING SITE FOR RESIDUE 15P A1228
11	BC2	SOFTWARE	TYR A:207 , TYR A:216 , GOL A:1225 , HOH A:2278 , HOH A:2335	BINDING SITE FOR RESIDUE 15P A1229
12	BC3	SOFTWARE	TYR A:150 , ILE A:154 , LYS A:155 , ASP A:156 , ALA A:157 , ASP A:176 , ARG A:178	BINDING SITE FOR RESIDUE MG A1231

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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 A from PDB  Type:PROTEIN  Length:217
 aligned with Q81YN8_BACAN | Q81YN8 from UniProtKB/TrEMBL  Length:245

    Alignment length:217
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       
         Q81YN8_BACAN    27 GIFIPNQISADRYEIKGVDVASYQGDIDWRELEKQNMKFAFIKATEGSAFVDKYFSKNWTNANKTSMRVGAYHFFSFDSKGETQAEQFIRNVPKYKQALPPVIDVEFYANKKDNPPKREDVTKELSVMIEMLEKHYGKKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWTFWQYTNRGKLSGYNGKEKYIDLNVFYGNEEEFENYGM 243
               SCOP domains d2waga_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------Glyco_hydro_25-2wagA01 A:19-194                                                                                                                                                 ------------------------ Pfam domains
         Sec.struct. author ...............eeeeehhhhh..hhhhhhh....eeeeeeee.......hhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhh.........eeee....hhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhh.......eeeee...............eeeee...............eeeee..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wag A   2 GSSHHHHHHMDRYEIKGVDVASYQGDIDWRELEKQNMKFAFIKATEGSAFVDKYFSKNWTNANKTSMRVGAYHFFSFDSKGETQAEQFIRNVPKYKQALPPVIDVEFYANKKDNPPKREDVTKELSVMIEMLEKHYGKKVILYATQEAYDLYIKDAYPQCDIWIRSVLTKPSLSDERKWTFWQYTNRGKLSGYNGKEKYIDLNVFYGNEEEFENYGM 218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (Q81YN8_BACAN | Q81YN8)

molecular function
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
	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:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	GO:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	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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