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Title :   PROTEIN CRYSTAL STRUCTURE OF XYLANASE A1 OF PAENIBACILLUS SP. JDR-2

Authors :   E. Pozharski, F. J. St John

Date :   01 Apr 11 (Deposition) - 04 Apr 12 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

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

Keywords :   (Beta/Alpha)8 Barrel, Gh10, Xylanase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. J. St John, J. F. Preston, E. Pozharski
Novel Structural Features Of Xylanase A1 From Paenibacillus Sp. Jdr-2.
J. Struct. Biol. V. 180 303 2012
PubMed-ID: 23000703 | Reference-DOI: 10.1016/J.JSB.2012.09.007

Molecule 1 - ENDO-1,4-BETA-XYLANASE
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETXYNA1CD
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	PJDR2_0221
	Organism Scientific	:	PAENIBACILLUS SP. JDR-2
	Organism Taxid	:	324057
	Strain	:	JDR-2

		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 (6, 21)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	GCV	2	Ligand/Ion	4-O-METHYL-ALPHA-D-GLUCURONIC ACID
3	GOL	9	Ligand/Ion	GLYCEROL
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	XYP	4	Ligand/Ion	BETA-D-XYLOPYRANOSE
6	XYS	2	Ligand/Ion	XYLOPYRANOSE

Biological Unit 1 (4, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GCV	1	Ligand/Ion	4-O-METHYL-ALPHA-D-GLUCURONIC ACID
3	GOL	5	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
6	XYS	1	Ligand/Ion	XYLOPYRANOSE

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GCV	1	Ligand/Ion	4-O-METHYL-ALPHA-D-GLUCURONIC ACID
3	GOL	4	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
6	XYS	1	Ligand/Ion	XYLOPYRANOSE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:90 , ALA A:91 , HOH A:524 , HOH A:573 , HOH A:685 , HOH A:706 , XYP B:343 , XYP B:344	BINDING SITE FOR RESIDUE GCV B 342
02	AC2	SOFTWARE	ASP A:50 , HOH A:425 , HOH A:439 , HOH A:549 , GCV B:342 , XYP B:344	BINDING SITE FOR RESIDUE XYP B 343
03	AC3	SOFTWARE	ASN B:45 , LYS B:48 , GLN B:88 , TRP B:305 , TRP B:313 , GCV B:342 , XYP B:343 , XYS B:345 , GOL B:346 , HOH B:436	BINDING SITE FOR RESIDUE XYP B 344
04	AC4	SOFTWARE	LYS B:48 , HIS B:81 , TRP B:85 , ASN B:137 , GLU B:138 , GLN B:232 , HIS B:234 , GLU B:262 , TRP B:305 , TRP B:313 , XYP B:344 , HOH B:517	BINDING SITE FOR RESIDUE XYS B 345
05	AC5	SOFTWARE	ALA A:20 , GLY A:44 , TRP A:305 , THR A:311 , SER A:312 , TRP A:313 , XYP A:344 , HOH A:467 , HOH A:547 , HOH A:704	BINDING SITE FOR RESIDUE GOL A 346
06	AC6	SOFTWARE	SER A:22 , ALA A:23 , ASN A:45 , MET A:67 , MG A:354 , HOH A:388 , HOH A:466 , HOH A:496 , HOH A:547 , HOH A:708 , HOH B:401	BINDING SITE FOR RESIDUE GOL A 347
07	AC7	SOFTWARE	ASN A:182 , PRO A:183 , SER A:184 , HOH A:500 , HOH A:552	BINDING SITE FOR RESIDUE CL A 348
08	AC8	SOFTWARE	ASN A:128 , LYS A:129 , SER A:184 , TRP A:185 , HOH A:360 , HOH A:499 , HOH A:500 , HOH A:535 , HOH A:572 , HOH A:598	BINDING SITE FOR RESIDUE GOL A 349
09	AC9	SOFTWARE	THR A:29	BINDING SITE FOR RESIDUE CL A 351
10	BC1	SOFTWARE	HIS A:86 , GLN A:87 , GLN A:88 , HOH A:540 , HOH A:549 , HOH A:569	BINDING SITE FOR RESIDUE GOL A 352
11	BC2	SOFTWARE	GLY A:107 , ARG A:108 , ASP A:109 , GLU A:110 , HOH A:398 , HOH A:511	BINDING SITE FOR RESIDUE GOL A 353
12	BC3	SOFTWARE	ILE A:21 , GLY A:44 , ASN A:45 , ALA A:46 , GOL A:347	BINDING SITE FOR RESIDUE MG A 354
13	BC4	SOFTWARE	XYP A:343 , XYP A:344 , PRO B:90 , ALA B:91 , GOL B:349 , HOH B:498 , HOH B:585	BINDING SITE FOR RESIDUE GCV A 342
14	BC5	SOFTWARE	GCV A:342 , XYP A:344 , ASP B:50 , HOH B:450 , HOH B:470 , HOH B:500 , HOH B:653 , HOH B:683	BINDING SITE FOR RESIDUE XYP A 343
15	BC6	SOFTWARE	ASN A:45 , LYS A:48 , GLN A:88 , TRP A:305 , TRP A:313 , GCV A:342 , XYP A:343 , XYS A:345 , GOL A:346 , HOH A:467	BINDING SITE FOR RESIDUE XYP A 344
16	BC7	SOFTWARE	LYS A:48 , HIS A:81 , TRP A:85 , ASN A:137 , GLU A:138 , GLN A:232 , HIS A:234 , GLU A:262 , TRP A:305 , TRP A:313 , XYP A:344 , HOH A:675	BINDING SITE FOR RESIDUE XYS A 345
17	BC8	SOFTWARE	GLY B:44 , TRP B:305 , THR B:311 , SER B:312 , TRP B:313 , XYP B:344 , HOH B:436 , HOH B:545 , HOH B:566	BINDING SITE FOR RESIDUE GOL B 346
18	BC9	SOFTWARE	SER B:22 , ALA B:23 , ASN B:45 , MET B:67 , HOH B:355 , HOH B:390 , HOH B:409 , HOH B:414 , HOH B:486 , HOH B:545	BINDING SITE FOR RESIDUE GOL B 347
19	CC1	SOFTWARE	LYS B:70 , ASN B:128 , TRP B:185 , HOH B:467 , HOH B:513 , HOH B:558 , HOH B:704 , HOH B:713	BINDING SITE FOR RESIDUE GOL B 348
20	CC2	SOFTWARE	GCV A:342 , GLN B:87 , GLN B:88 , SER B:89 , HOH B:683	BINDING SITE FOR RESIDUE GOL B 349

(no "SS Bond" information available for 3RDK)

Asymmetric Unit

No.	Residues
1	His A:81	-	Val A:82
2	His B:81	-	Val B:82

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

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.	XYNA1_PAESJ	768-778	2	A:255-265 B:255-265

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.	XYNA1_PAESJ	768-778	1	A:255-265 -

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.	XYNA1_PAESJ	768-778	1	- B:255-265

(no "Exon" information available for 3RDK)

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:333
 aligned with XYNA1_PAESJ | C6CRV0 from UniProtKB/Swiss-Prot  Length:1462

    Alignment length:333
                                   527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847   
          XYNA1_PAESJ   518 APLKDVYKNDFLIGNAISAEDLEGTRLELLKMHHDVVTAGNAMKPDALQPTKGNFTFTAADAMIDKVLAEGMKMHGHVLVWHQQSPAWLNTKKDDNNNTVPLGRDEALDNLRTHIQTVMKHFGNKVISWDVVNEAMNDNPSNPADYKASLRQTPWYQAIGSDYVEQAFLAAREVLDENPSWNIKLYYNDYNEDNQNKATAIYNMVKDINDRYAAAHNGKLLIDGVGMQGHYNINTNPDNVKLSLEKFISLGVEVSVSELDVTAGNNYTLPENLAVGQAYLYAQLFKLYKEHADHIARVTFWGMDDNTSWRAENNPLLFDKNLQAKPAYYGVID 850
               SCOP domains d3rdka_ A: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhh.eee.....eee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...........hhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh.......eeee..eee...hhhhhhhhhhhhhh...eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhh..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rdk A   5 APLKDVYKNDFLIGNAISAEDLEGTRLELLKMHHDVVTAGNAMKPDALQPTKGNFTFTAADAMIDKVLAEGMKMHGHVLVWHQQSPAWLNTKKDDNNNTVPLGRDEALDNLRTHIQTVMKHFGNKVISWDVVNEAMNDNPSNPADYKASLRQTPWYQAIGSDYVEQAFLAAREVLDENPSWNIKLYYNDYNEDNQNKATAIYNMVKDINDRYAAAHNGKLLIDGVGMQGHYNINTNPDNVKLSLEKFISLGVEVSVSELDVTAGNNYTLPENLAVGQAYLYAQLFKLYKEHADHIARVTFWGMDDNTSWRAENNPLLFDKNLQAKPAYYGVID 337
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334

Chain B from PDB  Type:PROTEIN  Length:334
 aligned with XYNA1_PAESJ | C6CRV0 from UniProtKB/Swiss-Prot  Length:1462

    Alignment length:334
                                   526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846    
          XYNA1_PAESJ   517 LAPLKDVYKNDFLIGNAISAEDLEGTRLELLKMHHDVVTAGNAMKPDALQPTKGNFTFTAADAMIDKVLAEGMKMHGHVLVWHQQSPAWLNTKKDDNNNTVPLGRDEALDNLRTHIQTVMKHFGNKVISWDVVNEAMNDNPSNPADYKASLRQTPWYQAIGSDYVEQAFLAAREVLDENPSWNIKLYYNDYNEDNQNKATAIYNMVKDINDRYAAAHNGKLLIDGVGMQGHYNINTNPDNVKLSLEKFISLGVEVSVSELDVTAGNNYTLPENLAVGQAYLYAQLFKLYKEHADHIARVTFWGMDDNTSWRAENNPLLFDKNLQAKPAYYGVID 850
               SCOP domains d3rdkb_ B: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhh.eee.....eee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...........hhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh.......eeee..eee...hhhhhhhhhhhhhh...eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhh..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rdk B   4 MAPLKDVYKNDFLIGNAISAEDLEGTRLELLKMHHDVVTAGNAMKPDALQPTKGNFTFTAADAMIDKVLAEGMKMHGHVLVWHQQSPAWLNTKKDDNNNTVPLGRDEALDNLRTHIQTVMKHFGNKVISWDVVNEAMNDNPSNPADYKASLRQTPWYQAIGSDYVEQAFLAAREVLDENPSWNIKLYYNDYNEDNQNKATAIYNMVKDINDRYAAAHNGKLLIDGVGMQGHYNINTNPDNVKLSLEKFISLGVEVSVSELDVTAGNNYTLPENLAVGQAYLYAQLFKLYKEHADHIARVTFWGMDDNTSWRAENNPLLFDKNLQAKPAYYGVID 337
                                    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       313       323       333

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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 '\|'

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: automated matches (180)

Protein domain: automated matches (180)

Paenibacillus sp. [TaxId: 324057] (2)

1a	d3rdka_	A:
1b	d3rdkb_	B:

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

(no "Pfam Domain" information available for 3RDK)

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYNA1_PAESJ | C6CRV0)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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:0016052	carbohydrate catabolic process	The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
	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: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.

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	Cis Peptide Bonds
		His A:81 - Val A:82	[ RasMol ]
		His B:81 - Val B:82	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (6, 21)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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