4BS0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF KEMP ELIMINASE HG3.17 E47N,N300D COMPLEXED WITH TRANSITION STATE ANALOG 6-NITROBENZOTRIAZOLE

Authors :   R. Blomberg, H. Kries, D. M. Pinkas, P. R. E. Mittl, M. G. Gruetter, H. K. P S. Mayo, D. Hilvert

Date :   06 Jun 13 (Deposition) - 16 Oct 13 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.09

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

Keywords :   Lyase-Lyase Inhibitor Complex, Computational Protein Design, Proton Transfer, Kemp Elimination, Directed Evolution, Transition State Tuning, Bottom-Up Enzyme Construction, Elementary Chemical Step Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Blomberg, H. Kries, D. M. Pinkas, P. R. E. Mittl, M. G. Gruetter, H. K. Privett, S. L. Mayo, D. Hilvert
Precision Is Essential For Efficient Catalysis In An Evolved Kemp Eliminase
Nature V. 503 418 2013
PubMed-ID: 24132235 | Reference-DOI: 10.1038/NATURE12623

Molecule 1 - KEMP ELIMINASE HG3.17
	Chains	:	A, B
	EC Number	:	4.-.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	GOLD
	Expression System Vector	:	PET-11B(PLUS)
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	THERMOASCUS AURANTIACUS
	Organism Taxid	:	5087
	Other Details	:	KEMP ELIMINASE HG-2 (PDB ID 3NYD) WITH MUTATION V6I, Q37K, K50Q, G82A, M84C, S89N, Q90F, T105I, A125T, T142N, T208M, S265T, F267M, W275A, R276F, T279S
	Other Details - Source	:	ENGINEERED ENZYME
	Synonym	:	ENDO-1,4-BETA-XYLANASE, XYLANASE, 1,4-BETA-D-XYLAN XYLANOHYDROLASE

		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, 6)

No.	Name	Count	Type	Full Name
1	6NT	2	Ligand/Ion	6-NITROBENZOTRIAZOLE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	6NT	1	Ligand/Ion	6-NITROBENZOTRIAZOLE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	6NT	1	Ligand/Ion	6-NITROBENZOTRIAZOLE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:57 , ASN A:60 , ARG B:118 , HOH B:2227 , HOH B:2396	BINDING SITE FOR RESIDUE SO4 B1303
2	AC2	SOFTWARE	ARG A:118 , HOH A:2267 , SER B:57 , ASN B:60 , HOH B:2114 , HOH B:2123 , HOH B:2399 , HOH B:2400	BINDING SITE FOR RESIDUE SO4 B1304
3	AC3	SOFTWARE	ARG A:161 , HOH A:2321 , HOH A:2324 , HOH A:2368	BINDING SITE FOR RESIDUE SO4 A1303
4	AC4	SOFTWARE	HIS A:88 , ARG A:140 , ASN A:142 , HOH A:2300 , HOH A:2301 , HOH A:2304	BINDING SITE FOR RESIDUE SO4 A1304
5	AC5	SOFTWARE	ALA A:21 , TRP A:44 , GLN A:50 , GLY A:83 , CYS A:84 , ASP A:127 , MET A:172 , LEU A:236 , MET A:237 , THR A:265	BINDING SITE FOR RESIDUE 6NT A1305
6	AC6	SOFTWARE	ALA B:21 , TRP B:44 , GLN B:50 , GLY B:83 , CYS B:84 , ASP B:127 , LEU B:236 , MET B:237 , THR B:265 , MET B:267	BINDING SITE FOR RESIDUE 6NT B1305

Asymmetric Unit

No.	Residues
1	A:255	-	A:261
2	B:255	-	B:261

Asymmetric Unit

No.	Residues
1	Gly A:83	-	Cys A:84
2	Gly B:83	-	Cys B:84

(no "SAP(SNP)/Variant" information available for 4BS0)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_THEAU	256-266	2	A:230-240 B:230-240

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_THEAU	256-266	1	A:230-240 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_THEAU	256-266	1	- B:230-240

(no "Exon" information available for 4BS0)

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:300
 aligned with XYNA_THEAU | P23360 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:300
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
           XYNA_THEAU    30 QSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGQVTPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIRGHTLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVNEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYINDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVAITELDVAGASPTDYVNVVNACLNVQSCVGITVWGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQ 329
               SCOP domains d4bs0a_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeeehhhhhh..hhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.............hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhh..hhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee....hhhh.hhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bs0 A   4 QSIDQLIKARGKVYFGVATDQNRLTTGKNAAIIKADFGMVWPENSMQWDATEPSQGNFNFAGADYLVNWAQQNGKLIGAGCLVWHNFLPSWVSSITDKNTLINVMKNHITTLMTRYKGKIRTWDVVGEAFNEDGSLRQNVFLNVIGEDYIPIAFQTARAADPNAKLYIMDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQMHLSAGQGAGVLQALPLLASAGTPEVSILMLDVAGASPTDYVNVVNACLNVQSCVGITVMGVADPDSAFASSTPLLFDGNFNPKPAYNAIVQDLQQ 303
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with XYNA_THEAU | P23360 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:300
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
           XYNA_THEAU    30 QSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGQVTPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIRGHTLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVNEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYINDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVAITELDVAGASPTDYVNVVNACLNVQSCVGITVWGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQ 329
               SCOP domains d4bs0b_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeeehhhhhh..hhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhh.hhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee....hhhh.hhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bs0 B   4 QSIDQLIKARGKVYFGVATDQNRLTTGKNAAIIKADFGMVWPENSMQWDATEPSQGNFNFAGADYLVNWAQQNGKLIGAGCLVWHNFLPSWVSSITDKNTLINVMKNHITTLMTRYKGKIRTWDVVGEAFNEDGSLRQNVFLNVIGEDYIPIAFQTARAADPNAKLYIMDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQMHLSAGQGAGVLQALPLLASAGTPEVSILMLDVAGASPTDYVNVVNACLNVQSCVGITVMGVADPDSAFASSTPLLFDGNFNPKPAYNAIVQDLQQ 303
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: beta-glycanases (284)

Protein domain: automated matches (49)

Thermoascus aurantiacus [TaxId: 5087] (3)

1a	d4bs0a_	A:
1b	d4bs0b_	B:

(no "CATH Domain" information available for 4BS0)

(no "Pfam Domain" information available for 4BS0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYNA_THEAU | P23360)

molecular function
	GO:0031176	endo-1,4-beta-xylanase activity	Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
	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.
	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.
	GO:0045493	xylan catabolic process	The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

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	Cis Peptide Bonds
		Gly A:83 - Cys A:84	[ RasMol ]
		Gly B:83 - Cys B:84	[ RasMol ]

Biological Units
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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