2VTF - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF THE ENDO-BETA-N-ACETYLGLUCOSAMINIDASE FROM ARTHROBACTER PROTOPHORMIAE E173Q MUTANT REVEALS A TIM BARREL CATALYTIC DOMAIN AND TWO ANCILLARY DOMAINS

Authors :   Z. Ling, R. J. Bingham, M. D. L. Suits, J. W. B. Moir, A. J. Fairbanks, E. J

Date :   14 May 08 (Deposition) - 31 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.79

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

Keywords :   Hydrolase, Family 85, Glycosidase, Arthrobacter, Carbohydrate Binding, Acetylglucosaminidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Suits, Z. Ling, R. J. Bingham, N. C. Bruce, G. J. Davies, A. J. Fairbanks, J. W. Moir, E. J. Taylor
The X-Ray Crystal Structure Of An Arthrobacter Protophormiae Endo-Beta-N-Acetylglucosaminidase Reveals A (Beta/Alpha)(8) Catalytic Domain, Two Ancillary Domains And Active Site Residues Key For Transglycosylation Activity.
J. Mol. Biol. V. 389 1 2009
PubMed-ID: 19327363 | Reference-DOI: 10.1016/J.JMB.2009.03.050

Molecule 1 - ENDO-BETA-N-ACETYLGLUCOSAMINIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.96
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 25-645
	Mutation	:	YES
	Organism Scientific	:	ARTHROBACTER PROTOPHORMIAE
	Organism Taxid	:	37930
	Strain	:	AKU0647

		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 (2, 8)

No.	Name	Count	Type	Full Name
1	B3P	4	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	B3P	2	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	B3P	2	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:37 , ARG A:115 , THR A:350 , SER A:353 , HOH A:2477 , HOH A:2740 , HOH A:2754 , HOH A:2755 , HOH A:2756 , HOH A:2757 , HOH A:2758 , HOH A:2759 , HOH A:2760 , HOH A:2761	BINDING SITE FOR RESIDUE B3P A1618
2	AC2	SOFTWARE	LEU A:135 , GLU A:139 , ASP A:178 , GLY A:180 , THR A:181 , HOH A:2233 , HOH A:2234 , HOH A:2237 , HOH A:2282 , HOH A:2283 , HOH A:2763 , HOH A:2764 , HOH A:2765 , HOH A:2766 , PHE B:12	BINDING SITE FOR RESIDUE B3P A1619
3	AC3	SOFTWARE	GLU B:139 , GLY B:180 , THR B:181 , HOH B:2199 , HOH B:2203	BINDING SITE FOR RESIDUE B3P B1620
4	AC4	SOFTWARE	GLU B:37 , ARG B:115 , THR B:350 , SER B:353 , HOH B:2421 , HOH B:2703 , HOH B:2727 , HOH B:2728 , HOH B:2729 , HOH B:2730 , HOH B:2731	BINDING SITE FOR RESIDUE B3P B1621
5	AC5	SOFTWARE	HIS B:54 , GLY B:199 , HIS B:201 , TYR B:266 , HOH B:2153 , HOH B:2732	BINDING SITE FOR RESIDUE PGE B1622
6	AC6	SOFTWARE	LYS B:373 , TYR B:563 , LYS B:568 , HIS B:596 , GLU B:598	BINDING SITE FOR RESIDUE PGE B1623
7	AC7	SOFTWARE	HIS A:54 , GLY A:199 , HIS A:201 , TYR A:266 , HOH A:2767	BINDING SITE FOR RESIDUE PGE A1620
8	AC8	SOFTWARE	TYR A:563 , LYS A:570 , GLU A:600	BINDING SITE FOR RESIDUE PGE A1621

(no "SS Bond" information available for 2VTF)

Asymmetric Unit

No.	Residues
1	Asp A:147	-	Gly A:148
2	Val A:354	-	Pro A:355
3	Arg A:393	-	Trp A:394
4	Val B:354	-	Pro B:355
5	Arg B:393	-	Trp B:394

(no "SAP(SNP)/Variant" information available for 2VTF)

(no "PROSITE Motif" information available for 2VTF)

(no "Exon" information available for 2VTF)

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:616
 aligned with Q9ZB22_9MICC | Q9ZB22 from UniProtKB/TrEMBL  Length:645

    Alignment length:616
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635      
         Q9ZB22_9MICC    26 TYNGPLSSHWFPEELAQWEPDSDPDAPFNRSHVPLEPGRVANRVNANADKDAHLVSLSALNRHTSGVPSQGAPVFYENTFSYWHYTDLMVYWAGSAGEGIIVPPSADVIDASHRNGVPILGNVFFPPTVYGGQLEWLEQMLEQEEDGSFPLADKLLEVADYYGFDGWFINQETEGADEGTAEAMQAFLVYLQEQKPEGMHIMWYDSMIDTGAIAWQNHLTDRNKMYLQNGSTRVADSMFLNFWWRDQRQSNELAQALGRSPYDLYAGVDVEARGTSTPVQWEGLFPEGEKAHTSLGLYRPDWAFQSSETMEAFYEKELQFWVGSTGNPAETDGQSNWPGMAHWFPAKSTATSVPFVTHFNTGSGAQFSAEGKTVSEQEWNNRSLQDVLPTWRWIQHGGDLEATFSWEEAFEGGSSLQWHGSLAEGEHAQIELYQTELPISEGTSLTWTFKSEHGNDLNVGFRLDGEEDFRYVEGEQRESINGWTQWTLPLDAFAGQTITGLAFAAEGNETGLAEFYIGQLAVGADSEKPAAPNVNVRQYDPDPSGIQLVWEKQSNVHHYRVYKETKHGKELIGTSAGDRIYLEGLVEESKQNDVRLHIEALSETFVPSDARMIDIK 641
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh.hhhhh.hhhhhh.........ee............eeeee.......................hhhhh.eeee.............hhhhhhhhhhh...eeeeeee.hhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh....eeeee..................hhhh.ee..ee...eeee......hhhhhhhhhhh..hhh.eeeeee...hhhhh..hhhhh.........eeeee..hhhhhh..hhhhhhhhhhhhhh................hhhhh...ee......eee.....ee..eee..eeee...ee.hhhh........eee..eeeeeee.........eeeeeee.....eeeeeeeeeeee.....eeeeeeee......eeeeee......eee...eeeee..eeeeeee.hhhh..eeeeeeeeee.....eeeeeeeeeeee..........eeeee.......eeeee.....eeeeeeee......eeeeee...eeee.hhhhhhhhh.eeeeeeeee........eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vtf A   2 TYNGPLSSHWFPEELAQWEPDSDPDAPFNRSHVPLEPGRVADRVNANADTDAHLVSLSALNRHTSGVPSQGAPVFYENTFSYWHYTDLMVYWAGSAGEGIIVPPSADVIDASHRNGVPILGNVFFPPTVYGGQLEWLEQMLEQEEDGSFPLADKLLEVADYYGFDGWFINQQTEGADEGTAEAMQAFLVYLQEQKPEGMHIMWYDSMIDTGAIAWQNHLTDRNKMYLQNGSTRVADSMFLNFWWRDQRQSNELAQALGRSPYDLYAGVDVEARGTSTPVQWEGLFPEGEKAHTSLGLYRPDWAFQSSETMEAFYEKELQFWVGSTGNPAETDGQSNWPGMAHWFPAKSTATSVPFVTHFNTGSGAQFSAEGKTVSEQEWNNRSLQDVLPTWRWIQHGGDLEATFSWEEAFEGGSSLQWHGSLAEGEHAQIELYQTELPISEGTSLTWTFKSEHGNDLNVGFRLDGEEDFRYVEGEQRESINGWTQWTLPLDAFAGQTITGLAFAAEGNETGLAEFYIGQLAVGADSEKPAAPNVNVRQYDPDPSGIQLVWEKQSNVHHYRVYKETKHGKELIGTSAGDRIYLEGLVEESKQNDVRLHIEALSETFVPSDARMIDIK 617
                                    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       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611

Chain B from PDB  Type:PROTEIN  Length:616
 aligned with Q9ZB22_9MICC | Q9ZB22 from UniProtKB/TrEMBL  Length:645

    Alignment length:620
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645
         Q9ZB22_9MICC    26 TYNGPLSSHWFPEELAQWEPDSDPDAPFNRSHVPLEPGRVANRVNANADKDAHLVSLSALNRHTSGVPSQGAPVFYENTFSYWHYTDLMVYWAGSAGEGIIVPPSADVIDASHRNGVPILGNVFFPPTVYGGQLEWLEQMLEQEEDGSFPLADKLLEVADYYGFDGWFINQETEGADEGTAEAMQAFLVYLQEQKPEGMHIMWYDSMIDTGAIAWQNHLTDRNKMYLQNGSTRVADSMFLNFWWRDQRQSNELAQALGRSPYDLYAGVDVEARGTSTPVQWEGLFPEGEKAHTSLGLYRPDWAFQSSETMEAFYEKELQFWVGSTGNPAETDGQSNWPGMAHWFPAKSTATSVPFVTHFNTGSGAQFSAEGKTVSEQEWNNRSLQDVLPTWRWIQHGGDLEATFSWEEAFEGGSSLQWHGSLAEGEHAQIELYQTELPISEGTSLTWTFKSEHGNDLNVGFRLDGEEDFRYVEGEQRESINGWTQWTLPLDAFAGQTITGLAFAAEGNETGLAEFYIGQLAVGADSEKPAAPNVNVRQYDPDPSGIQLVWEKQSNVHHYRVYKETKHGKELIGTSAGDRIYLEGLVEESKQNDVRLHIEALSETFVPSDARMIDIKSGSF 645
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------Glyco_hydro_85-2vtfB01 B:60-370                                                                                                                                                                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------Glyco_hydro_85-2vtfB02 B:60-370                                                                                                                                                                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........hhhhhhhhhhhhh.hhhhhh.........ee............eeeee.......................hhhhh.eeee.............hhhhhhhhhhh...eeeeeee.hhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh....eeeee..................hhhh.ee..ee...eeee......hhhhhhhhhhh..hhh.eeeeee...hhhhh..hhhhh.........eeeee..hhhhhh..hhhhhhhhhhhhhh................hhhhh...ee......eee.....ee..eee..eeee...ee.hhhh........eee..eeeeeee.........eeeeeee.....eeeeeeeeeeee.....eeeeeeee......eeeeee......eee...eeeee..eeeeeee.hhhh..eeeeeeeeee.....eeeeeeeeeeee...........eee........eeee......eeeeeeee.----.eeeeee...eeee.hhhhhhh...eeeeeeeee........eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vtf B   2 TYNGPLSSHWFPEELAQWEPDSDPDAPFNRSHVPLEPGRVADRVNANADTDAHLVSLSALNRHTSGVPSQGAPVFYENTFSYWHYTDLMVYWAGSAGEGIIVPPSADVIDASHRNGVPILGNVFFPPTVYGGQLEWLEQMLEQEEDGSFPLADKLLEVADYYGFDGWFINQQTEGADEGTAEAMQAFLVYLQEQKPEGMHIMWYDSMIDTGAIAWQNHLTDRNKMYLQNGSTRVADSMFLNFWWRDQRQSNELAQALGRSPYDLYAGVDVEARGTSTPVQWEGLFPEGEKAHTSLGLYRPDWAFQSSETMEAFYEKELQFWVGSTGNPAETDGQSNWPGMAHWFPAKSTATSVPFVTHFNTGSGAQFSAEGKTVSEQEWNNRSLQDVLPTWRWIQHGGDLEATFSWEEAFEGGSSLQWHGSLAEGEHAQIELYQTELPISEGTSLTWTFKSEHGNDLNVGFRLDGEEDFRYVEGEQRESINGWTQWTLPLDAFAGQTITGLAFAAEGNETGLAEFYIGQLAVGADSEKPAAPNVNVRQYDPDPSGIQLVWEKQSNVHHYRVYKE----KELIGTSAGDRIYLEGLVEESKQNDVRLHIEALSETFVPSDARMIDIKSGSF 619
                                    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       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561   |   569       579       589       599       609       619
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             565  568

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 '\|'

(no "SCOP Domain" information available for 2VTF)

(no "CATH Domain" information available for 2VTF)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Glyco_hydro_85] (1)

Family: Glyco_hydro_85 (1)

Arthrobacter protophormiae (1)

1a	Glyco_hydro_85-2vtfB01	B:60-370
1b	Glyco_hydro_85-2vtfB02	B:60-370

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9ZB22_9MICC | Q9ZB22)

molecular function
	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:0033925	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity	Catalysis of the endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg A:393 - Trp A:394	[ RasMol ]
		Arg B:393 - Trp B:394	[ RasMol ]
		Asp A:147 - Gly A:148	[ RasMol ]
		Val A:354 - Pro A:355	[ RasMol ]
		Val B:354 - Pro B:355	[ RasMol ]

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	2vtf
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	3.2.1.96
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	Q9ZB22_9MICC \| Q9ZB22	:	3fha 3fhq

(no "Related Entries Specified in the PDB File" available for 2VTF)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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SAPs(SNPs)/Variants (0, 0)

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