1GKK - JenaLib

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Title :   FERULOYL ESTERASE DOMAIN OF XYNY FROM CLOSTRIDIUM THERMOCELLUM

Authors :   J. A. M. Prates, N. Tarbouriech, S. J. Charnock, C. M. G. A. Fontes, L. M. A. Ferreira, G. J. Davies

Date :   15 Aug 01 (Deposition) - 13 Dec 01 (Release) - 07 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Hydrolase, Ferulic Acid, Esterase Family 1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. M. Prates, N. Tarbouriech, S. J. Charnock, C. M. G. A. Fontes, L. M. A. Ferreira, G. J. Davies
The Structure Of The Feruloyl Esterase Module Of Xylanase 10B From Clostridium Thermocellum Provides Insights Into Substrate Recognition
Structure V. 9 1183 2001
PubMed-ID: 11738044 | Reference-DOI: 10.1016/S0969-2126(01)00684-0

Molecule 1 - ENDO-1,4-BETA-XYLANASE Y
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	FERULOYL ESTERASE DOMAIN RESIDUES 792-1077
	Organism Scientific	:	CLOSTRIDIUM THERMOCELLUM
	Organism Taxid	:	1515
	Strain	:	YS
	Synonym	:	CBM22-2,XYLANASE Y, XYLY, 1,4-BETA-D-XYLAN XYLANOHYDROLASE Y

		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, 29)

No.	Name	Count	Type	Full Name
1	CD	10	Ligand/Ion	CADMIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
4	SEP	2	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:823 , HIS A:886 , MSE A:889 , HOH A:2161 , GLU B:1017	BINDING SITE FOR RESIDUE CD A3086
02	AC2	SOFTWARE	GLU A:894 , HIS A:1076 , GLU A:1079 , HIS A:1083 , HIS A:1085	BINDING SITE FOR RESIDUE CD A3087
03	AC3	SOFTWARE	GLU A:1007 , HOH A:2267 , HIS B:1082 , HIS B:1084	BINDING SITE FOR RESIDUE CD A3088
04	AC4	SOFTWARE	HIS A:947 , HIS A:1080 , HOH A:2226 , HOH A:2227 , HOH A:2337 , HOH A:2341	BINDING SITE FOR RESIDUE CD A3089
05	AC5	SOFTWARE	HIS A:1081 , HOH A:2342 , HOH A:2345 , HOH A:2349	BINDING SITE FOR RESIDUE CD A3090
06	AC6	SOFTWARE	GLU A:1017 , CYS B:823 , HIS B:886 , MSE B:889 , HOH B:2192	BINDING SITE FOR RESIDUE CD B3086
07	AC7	SOFTWARE	GLU B:894 , HIS B:1076 , GLU B:1079 , HIS B:1083 , HIS B:1085	BINDING SITE FOR RESIDUE CD B3087
08	AC8	SOFTWARE	HIS A:1082 , HIS A:1084 , GLU B:1007 , HOH B:2293	BINDING SITE FOR RESIDUE CD B3088
09	AC9	SOFTWARE	HIS B:947 , HIS B:1080 , HOH B:2250 , HOH B:2251 , HOH B:2358 , HOH B:2361	BINDING SITE FOR RESIDUE CD B3089
10	BC1	SOFTWARE	HIS B:1081 , HOH B:2366 , HOH B:2368 , HOH B:2374	BINDING SITE FOR RESIDUE CD B3090
11	BC2	SOFTWARE	LYS A:928 , GLU B:926 , SER B:927 , SER B:930 , HOH B:2232 , HOH B:2233 , HOH B:2237	BINDING SITE FOR RESIDUE GOL B3091

(no "SS Bond" information available for 1GKK)

(no "Cis Peptide Bond" information available for 1GKK)

(no "SAP(SNP)/Variant" information available for 1GKK)

(no "PROSITE Motif" information available for 1GKK)

(no "Exon" information available for 1GKK)

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:283
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:283
                                                                                                                                                                                                                                                                                                           1077        
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072    |    -   
          XYNY_CLOTM    803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLMHGGGENENTIFSNDVKLQNILDHAIMNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRMHRGFGGFSMGGLTTWYVMVNCLDYVAYFMPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSDHIAYANMNPQIEAMKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHE--------    -
               SCOP domains d1gkka_ A: Feruloyl esterase domain of the cellulosomal xylanase y                                                                                                                                                                                                                          SCOP domains
               CATH domains 1gkkA00 A:803-1085  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh......eeeeeeeee..eeeeeeeee..........eeeeee...............hhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhh.......hhhhhhhh...eeeeeehhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhhh..............eeeeee.....hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gkk A  803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLmHGGGENENTIFSNDVKLQNILDHAImNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRmHRGFGGFsmGGLTTWYVmVNCLDYVAYFmPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSEDIAYANmNPQIEAmKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHELEHHHHHH 1085
                                   812       822       832       842       852       862|      872       882      |892       902       912       922       932       942   |   952 ||    962 |     972  |    982       992      1002      1012      1022 |    1032      1042      1052      1062      1072      1082   
                                                                                      863-MSE                   889-MSE                                                  946-MSE 954-SEP   964-MSE    975-MSE                                         1024-MSE  |                                                      
                                                                                                                                                                                  955-MSE                                                                    1031-MSE

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with XYNY_CLOTM | P51584 from UniProtKB/Swiss-Prot  Length:1077

    Alignment length:283
                                                                                                                                                                                                                                                                                                           1077        
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072    |    -   
          XYNY_CLOTM    803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLMHGGGENENTIFSNDVKLQNILDHAIMNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRMHRGFGGFSMGGLTTWYVMVNCLDYVAYFMPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSDHIAYANMNPQIEAMKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHE--------    -
               SCOP domains d1gkkb_ B: Feruloyl esterase domain of the cellulosomal xylanase y                                                                                                                                                                                                                          SCOP domains
               CATH domains 1gkkB00 B:803-1085  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh......eeeeeeeee..eeeeeeeee...........eeeee...............hhhhhhhhhhhh......eeee...........hhhhhhhhhhhhhhhhhh.......hhhhhhhh...eeeeeehhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhhhhhhhhh..............eeeeee.....hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gkk B  803 SFKYESAVQYRPAPDSYLNPCPQAGRIVKETYTGINGTKSLNVYLPYGYDPNKKYNIFYLmHGGGENENTIFSNDVKLQNILDHAImNGELEPLIVVTPTFNGGNCTAQNFYQEFRQNVIPFVESKYSTYAESTTPQGIAASRmHRGFGGFsmGGLTTWYVmVNCLDYVAYFmPLSGDYWYGNSPQDKANSIAEAINRSGLSKREYFVFAATGSEDIAYANmNPQIEAmKALPHFDYTSDFSKGNFYFLVAPGATHWWGYVRHYIYDALPYFFHELEHHHHHH 1085
                                   812       822       832       842       852       862|      872       882      |892       902       912       922       932       942   |   952 ||    962 |     972  |    982       992      1002      1012      1022 |    1032      1042      1052      1062      1072      1082   
                                                                                      863-MSE                   889-MSE                                                  946-MSE 954-SEP   964-MSE    975-MSE                                         1024-MSE  |                                                      
                                                                                                                                                                                  955-MSE                                                                    1031-MSE

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	-	→ 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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Carboxylesterase (24)

Protein domain: Feruloyl esterase domain of the cellulosomal xylanase y (5)

Clostridium thermocellum [TaxId: 1515] (5)

1a	d1gkka_	A:
1b	d1gkkb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Clostridium thermocellum. Organism_taxid: 1515. Strain: ys. (2)

1a	1gkkA00	A:803-1085
1b	1gkkB00	B:803-1085

(no "Pfam Domain" information available for 1GKK)

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYNY_CLOTM | P51584)

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.
cellular component
	GO:0043263	cellulosome	An extracellular multi-enzyme complex containing up to 11 different enzymes aligned on a non-catalytic scaffolding glycoprotein. Functions to hydrolyze cellulose.

Asymmetric Unit
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	1gkk
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	XYNY_CLOTM \| P51584
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1dyo	XYLAN-BINDING DOMAIN FROM CBM 22, FORMALLY X6B DOMAIN
1gkl	S954A MUTANT OF THE FERULOYL ESTERASE MODULE FROM CLOSTRIDIUM THERMOCELLUM COMPLEXED WITH FERULIC ACID
1h6x	THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING
1h6y	THE ROLE OF CONSERVED AMONI ACIDS IN THE CLEFT OF THE C-TERMINAL FAMILY 22 CARBOHYDRATE BINDING MODULE OF CLOSTRIDIUM THERMOCELLUM XYN10B IN LIGAND BINDING

Description

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Ligands, Modified Residues, Ions (4, 29)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (9, 9)

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