4AZI - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE, STRH

Authors :   B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston

Date :   26 Jun 12 (Deposition) - 10 Jul 13 (Release) - 13 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Inhibition Of The Family 20 Glycoside Hydrolase Catalytic Modules In The Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh.
Org. Biomol. Chem. V. 11 7907 2013
PubMed-ID: 24132305 | Reference-DOI: 10.1039/C3OB41579A

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC MODULE, RESIDUES 627-1064
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	170187
	Strain	:	TIGR4
	Synonym	:	GLYCOSIDE HYDROLASE 20

		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 (4, 15)

No.	Name	Count	Type	Full Name
1	BCN	3	Ligand/Ion	BICINE
2	BR	4	Ligand/Ion	BROMIDE ION
3	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
4	OAN	2	Ligand/Ion	O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	BCN	1	Ligand/Ion	BICINE
2	BR	-1	Ligand/Ion	BROMIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	OAN	1	Ligand/Ion	O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	BCN	2	Ligand/Ion	BICINE
2	BR	-1	Ligand/Ion	BROMIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	OAN	1	Ligand/Ion	O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:641 , HIS A:742 , ASP A:804 , GLU A:805 , TRP A:872 , TYR A:902 , ILE A:904 , TYR A:914 , TRP A:951 , ASP A:953 , EDO A:2041 , HOH A:3047 , HOH A:3565 , HOH A:3566	BINDING SITE FOR RESIDUE OAN A2038
02	AC2	SOFTWARE	HIS A:625 , ASN A:1020 , ASN A:1022 , LYS A:1023 , HOH A:3520	BINDING SITE FOR RESIDUE EDO A2039
03	AC3	SOFTWARE	GLN A:716 , LYS A:795 , HOH A:3113 , HOH A:3199 , HOH A:3569	BINDING SITE FOR RESIDUE EDO A2040
04	AC4	SOFTWARE	HIS A:742 , GLU A:805 , ASN A:808 , OAN A:2038 , HOH A:3016 , HOH A:3565	BINDING SITE FOR RESIDUE EDO A2041
05	AC5	SOFTWARE	PHE A:915 , LEU A:916 , LYS A:917	BINDING SITE FOR RESIDUE BR A2042
06	AC6	SOFTWARE	PRO A:955 , SER A:956	BINDING SITE FOR RESIDUE BR A2043
07	AC7	SOFTWARE	GLN A:823 , TYR A:825 , GLY A:826	BINDING SITE FOR RESIDUE BR A2044
08	AC8	SOFTWARE	THR A:834 , ALA A:837 , MET A:838 , GLU A:841 , HOH A:3230	BINDING SITE FOR RESIDUE BCN A2045
09	AC9	SOFTWARE	ARG B:641 , HIS B:742 , ASP B:804 , GLU B:805 , PHE B:849 , TRP B:872 , TYR B:902 , ILE B:904 , TRP B:913 , TYR B:914 , TRP B:951 , ASP B:953 , EDO B:2043 , BCN B:2046 , HOH B:3049	BINDING SITE FOR RESIDUE OAN B2040
10	BC1	SOFTWARE	ARG B:954 , PRO B:955 , HOH B:3445	BINDING SITE FOR RESIDUE EDO B2041
11	BC2	SOFTWARE	HOH B:3131	BINDING SITE FOR RESIDUE EDO B2042
12	BC3	SOFTWARE	ARG B:641 , HIS B:742 , GLU B:805 , ASN B:808 , OAN B:2040 , BCN B:2046	BINDING SITE FOR RESIDUE EDO B2043
13	BC4	SOFTWARE	TYR B:854 , GLN B:862 , LYS B:890 , HOH B:3325	BINDING SITE FOR RESIDUE BR B2044
14	BC5	SOFTWARE	HIS B:974 , HOH B:3385 , HOH B:3476	BINDING SITE FOR RESIDUE BCN B2045
15	BC6	SOFTWARE	ALA B:813 , TRP B:913 , TYR B:914 , OAN B:2040 , EDO B:2043 , HOH B:3187 , HOH B:3534 , HOH B:3535	BINDING SITE FOR RESIDUE BCN B2046

(no "SS Bond" information available for 4AZI)

Asymmetric Unit

No.	Residues
1	Ser A:739	-	Pro A:740
2	Tyr A:936	-	Pro A:937
3	Ser B:739	-	Pro B:740
4	Tyr B:936	-	Pro B:937

(no "SAP(SNP)/Variant" information available for 4AZI)

(no "PROSITE Motif" information available for 4AZI)

(no "Exon" information available for 4AZI)

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:410
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:415
                                   632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032     
          STRH_STRPN    623 KREVEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGGGFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKIPTNLEGYSKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAA 1037
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhheeeeeee......hhhhhhhhhhhhhhhh..eeeeeee............eee..eeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh.....eee...eeeeee...hhhhhhhhhhhhhhhhhhhh....eeeee....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeee....hhhhh.........eeee...........hhhhhhhh..eeee.hhh.eee...hhhhh..hhhhhhhhhhhh................eeeeeeeee........hhhhhhhhhhhhhhhh.......hhhhhhhhh...-----.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4azi A  623 GSHMEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGWYFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKIP-----YSKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAA 1037
                                   632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992 |    1002      1012      1022      1032     
                                                                                                                                                                                                                                                                                                                                                                                                             994  1000

Chain B from PDB  Type:PROTEIN  Length:408
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:417
                                   632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032       
          STRH_STRPN    623 KREVEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGGGFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKIPTNLEGYSKESLEALDAAKTALNYNLNRNKQAELDTLVANLKAALQ 1039
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhheeeeeee......hhhhhhhhhhhhhhhh..eeeeeee............eee..eeehhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh.....eee...eeeeee...hhhhhhhhhhhhhhhhhhhh....eeeee....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeee....hhhhh.........eeee...........hhhhhhhh..eeee.hhhhhee...hhhhh..hhhhhhhhhhhh................eeeeeeeee........hhhhhhhhhhhhhhh........hhhhhhhhhh.---------hhhhhhhhhhhh........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4azi B  623 GSHMEKLAKNKVISIDAGRKYFTLNQLKRIVDKASELGYSDVHLLLGNDGLRFLLDDMTITANGKTYASDDVKKAIIEGTKAYYDDPNGTALTQAEVTELIEYAKSKDIGLIPAINSPGHMDAMLVAMEKLGIKNPQAHFDKVSKTTMDLKNEEAMNFVKALIGKYMDFFAGKTKIFNFGTDEYANDATSAQGWYYLKWYQLYGKFAEYANTLAAMAKERGLQPMAFNDGFYYEDKDDVQFDKDVLISYWSKGWWGYNLASPQYLASKGYKFLNTNGDWYYILGQKPEDGWYFLKKAIENTGKTPFNQLASTKYPEVDLPTVGSMLSIWADRPSAEYKEEEIFELMTAFADHNKDYFRANYNALREELAKI---------ESLEALDAAKTALNYNLNRNKQAELDTLVANLKAALQ 1039
                                   632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992|        -|     1012      1022      1032       
                                                                                                                                                                                                                                                                                                                                                                                                            993      1003

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 '\|'

(no "SCOP Domain" information available for 4AZI)

(no "CATH Domain" information available for 4AZI)

(no "Pfam Domain" information available for 4AZI)

Asymmetric Unit(hide GO term definitions)

Chain A,B (STRH_STRPN | P49610)

molecular function
	GO:0004563	beta-N-acetylhexosaminidase activity	Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
	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.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-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.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ser A:739 - Pro A:740	[ RasMol ]
		Ser B:739 - Pro B:740	[ RasMol ]
		Tyr A:936 - Pro A:937	[ RasMol ]
		Tyr B:936 - Pro B:937	[ RasMol ]

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Access by PDB/NDB ID
	4azi
		Family and Domain Information	:	ProDom \| SYSTERS
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	STRH_STRPN \| P49610
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	3.2.1.52
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	STRH_STRPN \| P49610
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UniProtKB/Swiss-Prot
	STRH_STRPN \| P49610	:	2ltj 2yl5 2yl6 2yl8 2yl9 2yla 2yll 4az5 4az6 4az7 4azb 4azc 4azg 4azh

2yl5	INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl6	INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl8	INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl9	INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yla	INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yll	INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
4az5	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az6	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az7	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azb	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azc	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azg	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azh	DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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