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Title :   CRYSTAL STRUCTURE OF UNSATURATED GLUCURONYL HYDROLASE MUTANT D175N FROM STREPTCOCCUS AGALACTIAE COMPLEXED WITH DGLCA-GALNAC6S

Authors :   Y. Nakamichi, Y. Maruyama, B. Mikami, W. Hashimoto, K. Murata

Date :   02 Sep 10 (Deposition) - 06 Oct 10 (Release) - 16 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

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

Keywords :   Alpha6/Alpha6-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Nakamichi, Y. Maruyama, B. Mikami, W. Hashimoto, K. Murata
Structural Determinants In Streptococcal Unsaturated Glucuronyl Hydrolase For Recognition Of Glycosaminoglycan Sulfate Groups
J. Biol. Chem. V. 286 6262 2011
PubMed-ID: 21147778 | Reference-DOI: 10.1074/JBC.M110.182618

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN GBS1889
	Chains	:	A
	EC Number	:	3.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Strain	:	HMS174
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GBS1889, UGL
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS AGALACTIAE
	Organism Taxid	:	216495
	Strain	:	SEROGROUP III/NEM316
	Synonym	:	UNSATURATED GLUCURONYL HYDROLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	GCD	1	Ligand/Ion	4,5-DEHYDRO-D-GLUCURONIC ACID
3	NG6	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE 6-SULFATE

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	GCD	1	Ligand/Ion	4,5-DEHYDRO-D-GLUCURONIC ACID
3	NG6	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE 6-SULFATE

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
2	GCD	2	Ligand/Ion	4,5-DEHYDRO-D-GLUCURONIC ACID
3	NG6	2	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE 6-SULFATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:115 , GLY A:233 , THR A:235 , TYR A:364 , SER A:365 , SER A:368 , LYS A:370 , GCD A:400	BINDING SITE FOR RESIDUE NG6 A 399
2	AC2	SOFTWARE	TRP A:69 , ASP A:115 , PHE A:118 , ASN A:175 , TRP A:245 , ARG A:247 , TRP A:251 , NG6 A:399	BINDING SITE FOR RESIDUE GCD A 400
3	AC3	SOFTWARE	LEU A:19 , GLU A:330 , TYR A:334	BINDING SITE FOR RESIDUE EDO A 3318
4	AC4	SOFTWARE	ARG A:196 , TYR A:204 , MET A:263	BINDING SITE FOR RESIDUE EDO A 401
5	AC5	SOFTWARE	ILE A:4 , LYS A:5 , PRO A:6 , VAL A:7 , GLN A:267	BINDING SITE FOR RESIDUE EDO A 402
6	AC6	SOFTWARE	TYR A:260 , LYS A:264 , TYR A:266 , ASP A:393 , HOH A:425	BINDING SITE FOR RESIDUE EDO A 403
7	AC7	SOFTWARE	LEU A:319 , LYS A:320 , LYS A:329 , HOH A:435 , HOH A:526	BINDING SITE FOR RESIDUE EDO A 404

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

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

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

(no "PROSITE Motif" information available for 3ANK)

(no "Exon" information available for 3ANK)

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:377
 aligned with UCDH_STRA3 | Q8E372 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:397
                                    11        21        31        41        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       311       321       331       341       351       361       371       381       391       
           UCDH_STRA3     2 MKIKPVKVESIENPKRFLNSRLLTKIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLAYEYNQDKKLKNIAHKNVLSFLNRINNRIALDHHDLGFLYTPSCTAEYRINGDVKALEATIKAADKLMERYQEKGGFIQAWGELGYKEHYRLIIDCLLNIQLLFFAYEQTGDEKYRQVAVNHFYASANNVVRDDSSAFHTFYFDPETGEPLKGVTRQGYSDESSWARGQAWGIYGIPLSYRKMKDYQQIILFKGMTNYFLNRLPEDKVSYWDLIFTDGSGQPRDTSATATAVCGIHEMLKYLPEVDPDKETYKYAMHTMLRSLIEQYSNNELIAGRPLLLHGVYSWHSGKGVDEGNIWGDYYYLEALIRFYKDWELYW 398
               SCOP domains d3anka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..ee..........ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh--------------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............eeee....eeeee.hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ank A   2 MKIKPVKVESIENPKRFLNSRLLTKIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLAYEYNQDKKLKNIAHKNVLSFLNRINNRIALDHHDLGFLYTPSCTAEYRINGDVKALEATIKAADKLMERY--------------------LIINCLLNIQLLFFAYEQTGDEKYRQVAVNHFYASANNVVRDDSSAFHTFYFDPETGEPLKGVTRQGYSDESSWARGQAWGIYGIPLSYRKMKDYQQIILFKGMTNYFLNRLPEDKVSYWDLIFTDGSGQPRDTSATATAVCGIHEMLKYLPEVDPDKETYKYAMHTMLRSLIEQYSNNELIAGRPLLLHGVYSWHSGKGVDEGNIWGDYYYLEALIRFYKDWELYW 398
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         -         -|      181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       
                                                                                                                                                                               151                  172

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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha/alpha toroid (324)

Superfamily: Six-hairpin glycosidases (109)

Family: automated matches (16)

Protein domain: automated matches (16)

Streptococcus agalactiae [TaxId: 216495] (3)

d3anka_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (UCDH_STRA3 | Q8E372)

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:0052757	chondroitin hydrolase activity	Catalysis of the hydrolysis of hexosaminic linkages in chondroitin, a linear polymer structure composed of the repeating disaccharide unit [->4)-D-glucuronic acid-(1->3)-N-acetyl-D-galactosamine-(1-], also written as [->4GlcUA1->3GalNAc1-].
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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	UCDH_STRA3 \| Q8E372
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	3.2.1.-
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	UCDH_STRA3 \| Q8E372	:	3ani 3anj 3vxd 3wux

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (8, 8)

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