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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF KEMP ELIMINASE HG-2 COMPLEXED WITH TRANSITION STATE ANALOG 5-NITRO BENZOTRIAZOLE

Authors :   T. M. Lee, H. K. Privett, J. T. Kaiser, S. L. Mayo

Date :   14 Jul 10 (Deposition) - 29 Jun 11 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.23

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tim Barrel, Kemp Elimination Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. K. Privett, G. Kiss, T. M. Lee, R. Blomberg, R. A. Chica, L. M. Thomas, D. Hilvert, K. N. Houk, S. L. Mayo
Iterative Approach To Computational Enzyme Design.
Proc. Natl. Acad. Sci. Usa V. 109 3790 2012
PubMed-ID: 22357762 | Reference-DOI: 10.1073/PNAS.1118082108

Molecule 1 - ENDO-1,4-BETA-XYLANASE
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 27-329
	Gene	:	XYLANASE I, XYNA
	Mutation	:	YES
	Organism Scientific	:	THERMOASCUS AURANTIACUS
	Organism Taxid	:	5087
	Synonym	:	XYLANASE, 1,4-BETA-D-XYLAN XYLANOHYDROLASE, TAXI

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	3NY	2	Ligand/Ion	5-NITRO-1H-BENZOTRIAZOLE
2	ACT	4	Ligand/Ion	ACETATE ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:21 , TRP A:44 , PRO A:45 , GLY A:82 , GLY A:83 , MET A:84 , ASP A:127 , LEU A:236 , MET A:237 , SER A:265 , PHE A:267 , HOH A:879	BINDING SITE FOR RESIDUE 3NY A 317
2	AC2	SOFTWARE	TRP A:44 , ALA A:125 , ASP A:127 , TYR A:170 , SER A:234 , LEU A:236 , HOH A:482	BINDING SITE FOR RESIDUE ACT A 318
3	AC3	SOFTWARE	PRO A:56 , SER A:57 , ASN A:60 , HOH A:533 , HOH A:550 , HOH A:741 , HOH A:864 , ARG B:118	BINDING SITE FOR RESIDUE ACT A 319
4	AC4	SOFTWARE	GLN A:58 , ASN A:106 , THR A:246 , VAL A:249 , HOH A:379 , HOH A:530 , HOH A:531	BINDING SITE FOR RESIDUE ACT A 320
5	AC5	SOFTWARE	ARG A:161 , HOH A:521 , HOH A:790	BINDING SITE FOR RESIDUE SO4 A 321
6	AC6	SOFTWARE	ARG A:118 , HOH A:331 , HOH A:649 , HOH A:748 , HOH A:800 , SER B:57 , ASN B:60	BINDING SITE FOR RESIDUE SO4 A 322
7	AC7	SOFTWARE	ALA B:21 , TRP B:44 , PRO B:45 , GLY B:82 , GLY B:83 , MET B:84 , ASP B:127 , LEU B:236 , MET B:237 , SER B:265 , PHE B:267	BINDING SITE FOR RESIDUE 3NY B 317
8	AC8	SOFTWARE	TRP B:44 , ALA B:125 , ASP B:127 , TYR B:170 , GLY B:205 , SER B:234 , LEU B:236 , HOH B:373	BINDING SITE FOR RESIDUE ACT B 318

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_2	PS51760	Glycosyl hydrolases family 10 (GH10) domain profile.	XYNA_THEAU	29-326	2	A:3-300 B:3-300
2	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_THEAU	256-266	2	A:230-240 B:230-240

(no "Exon" information available for 3NYD)

Asymmetric/Biological 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:304
 aligned with XYNA_THEAU | P23360 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:304
                                                                                                                                                                                                                                                                                                                                        329 
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326  | 
           XYNA_THEAU    27 QAAQSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGQVTPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIRGHTLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVNEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYINDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVAITELDVAGASPTDYVNVVNACLNVQSCVGITVWGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQ-   -
               SCOP domains d3nyda_ A: 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...hhhhh.hhhhh..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GH10_2  PDB: A:3-300 UniProt: 29-326                                                                                                                                                                                                                                                                      ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ---------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nyd A   1 EAAQSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGMVWPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIGGGMLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVGEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYIMDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVSILMLDVAGASPTDYVNVVNACLNVQSCVGISVFGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQG 304
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with XYNA_THEAU | P23360 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:301
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 
           XYNA_THEAU    29 AQSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGQVTPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIRGHTLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVNEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYINDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVAITELDVAGASPTDYVNVVNACLNVQSCVGITVWGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQ 329
               SCOP domains d3nydb_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Glyco_hydro_10-3nydB01 B:5-301                                                                                                                                                                                                                                                                           -- Pfam domains (1)
           Pfam domains (2) --Glyco_hydro_10-3nydB02 B:5-301                                                                                                                                                                                                                                                                           -- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh...eeeeeehhhhhh..hhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeee.........hhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhh.hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GH10_2  PDB: B:3-300 UniProt: 29-326                                                                                                                                                                                                                                                                      --- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     --------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nyd B   3 AQSVDQLIKARGKVYFGVATDQNRLTTGKNAAIIQADFGMVWPENSMKWDATEPSQGNFNFAGADYLVNWAQQNGKLIGGGMLVWHSQLPSWVSSITDKNTLTNVMKNHITTLMTRYKGKIRAWDVVGEAFNEDGSLRQTVFLNVIGEDYIPIAFQTARAADPNAKLYIMDYNLDSASYPKTQAIVNRVKQWRAAGVPIDGIGSQTHLSAGQGAGVLQALPLLASAGTPEVSILMLDVAGASPTDYVNVVNACLNVQSCVGISVFGVADPDSWRASTTPLLFDGNFNPKPAYNAIVQDLQQ 303
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302

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/Biological 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	d3nyda_	A:
1b	d3nydb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_10 (42)

Thermoascus aurantiacus (3)

1a	Glyco_hydro_10-3nydB01	B:5-301
1b	Glyco_hydro_10-3nydB02	B:5-301

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:83 - Met A:84	[ RasMol ]
		Gly B:83 - Met B:84	[ RasMol ]

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	3nyd
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	XYNA_THEAU \| P23360
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	3.2.1.8
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	XYNA_THEAU \| P23360
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	XYNA_THEAU \| P23360	:	1gok 1gom 1goo 1goq 1gor 1i1w 1i1x 1k6a 1tux 2bnj 3o2l 4bs0

(no "Related Entries Specified in the PDB File" available for 3NYD)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 2)

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