Endo-1,4-beta-xylanase A precursor - Clostridium stercorarium

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Reviewed, UniProtKB/Swiss-Prot Q8GJ44 (XYNA1_CLOSR)

Last modified November 25, 2008. Version 38. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Endo-1,4-beta-xylanase A
    EC=3.2.1.8
Alternative name(s):
    Xylanase 11A
      Short name=Xyn11A
    1,4-beta-D-xylan xylanohydrolase A

Gene names

Name:

xynA

Organism

Clostridium stercorarium

Taxonomic identifier

1510 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

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Protein attributes

Sequence length	651 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Endoxylanase that degrades arabinoxylan and glucuronoxylan to xylobiose and xylotriose (in vitro).
Catalytic activity	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
Pathway	Glycan degradation; xylan degradation.
Subcellular location	Secreted.
Induction	Up-regulated by growth on xylan.
Domain	XynA is a modular enzyme. The number of CBM6 (carbohydrate binding type-6) domains varies between strains. The polymeric substrate can interact with several of these CBM6 domains.
Sequence similarities	Belongs to the glycosyl hydrolase 11 (cellulase G) family. Contains 3 CBM6 (carbohydrate binding type-6) domains.
Biophysicochemical properties	pH dependence: Optimum pH is 6.5-7.0. Temperature dependence: Optimum temperature is 75 degrees Celsius. Thermostable.

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Ontologies

Keywords
Biological process	Carbohydrate metabolism Cellulose degradation Polysaccharide degradation Xylan degradation
Cellular component	Secreted
Domain	Repeat Signal
Ligand	Calcium Metal-binding
Molecular function	Glycosidase Hydrolase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	cellulose catabolic process Inferred from electronic annotation. Source: UniProtKB-KW xylan catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	extracellular region Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	calcium ion binding Inferred from electronic annotation. Source: UniProtKB-KW carbohydrate binding Inferred from electronic annotation. Source: InterPro endo-1,4-beta-xylanase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 30

Potential

Chain

31 – 651

621

Endo-1,4-beta-xylanase A

PRO_0000236809

Regions

Domain

250 – 370

121

CBM6 1

Repeat

278 – 339

Domain

387 – 507

121

CBM6 2

Repeat

415 – 476

Domain

527 – 647

121

CBM6 3

Repeat

555 – 616

Region

278 – 616

339

3 X 61 AA approximate repeats

Sites

Active site

124

Nucleophile By similarity

Active site

214

Proton donor By similarity

Metal binding

253

Calcium 1

Metal binding

255

Calcium 1

Metal binding

275

Calcium 1; via carbonyl oxygen

Metal binding

365

Calcium 1

Metal binding

530

Calcium 2

Metal binding

532

Calcium 2

Metal binding

552

Calcium 2; via carbonyl oxygen

Metal binding

642

Calcium 2

Binding site

270

Substrate 1; via carbonyl oxygen

Binding site

279

Substrate 1; via amide nitrogen

Binding site

336

Substrate 1

Binding site

363

Substrate 1

Binding site

556

Substrate 2; via amide nitrogen

Binding site

613

Substrate 2

Binding site

640

Substrate 2

Experimental info

Sequence conflict

649 – 651

SGT → FRNLRV in CAD48307. Ref.1

Secondary structure

651

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q8GJ44-1 [UniParc].

Last modified May 30, 2006. Version 2.
Checksum: 52E501A16F9D1423
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FASTA

651

70,151

        10         20         30         40         50         60 
MKRKVKKMAA MATSIIMAIM IILHSIPVLA GRIIYDNETG THGGYDYELW KDYGNTIMEL 

        70         80         90        100        110        120 
NDGGTFSCQW SNIGNALFRK GRKFNSDKTY QELGDIVVEY GCDYNPNGNS YLCVYGWTRN 

       130        140        150        160        170        180 
PLVEYYIVES WGSWRPPGAT PKGTITVDGG TYEIYETTRV NQPSIDGTAT FQQYWSVRTS 

       190        200        210        220        230        240 
KRTSGTISVT EHFKQWERMG MRMGKMYEVA LTVEGYQSSG YANVYKNEIR IGANPTPAPS 

       250        260        270        280        290        300 
QSPIRRDAFS IIEAEEYNST NSSTLQVIGT PNNGRGIGYI ENGNTVTYSN IDFGSGATGF 

       310        320        330        340        350        360 
SATVATEVNT SIQIRSDSPT GTLLGTLYVS STGSWNTYQT VSTNISKITG VHDIVLVFSG 

       370        380        390        400        410        420 
PVNVDNFIFS RSSPVPAPGD NTRDAYSIIQ AEDYDSSYGP NLQIFSLPGG GSAIGYIENG 

       430        440        450        460        470        480 
YSTTYNNVNF ANGLSSITAR VATQISTSIQ VRAGGATGTL LGTIYVPSTN SWDSYQNVTA 

       490        500        510        520        530        540 
NLSNITGVHD ITLVFSGPVN VDYFVFTPAN VNSGPTSPVG GTRSAFSNIQ AEDYDSSYGP 

       550        560        570        580        590        600 
NLQIFSLPGG GSAIGYIENG YSTTYKNIDF GDGATSVTAR VATQNATTIQ VRLGSPSGTL 

       610        620        630        640        650 
LGTIYVGSTG SFDTYRDVSA TISNTAGVKD IVLVFSGPVN VDWFVFSKSG T

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References

[1]	"Enzyme system of Clostridium stercorarium for hydrolysis of arabinoxylan: reconstitution of the in vivo system from recombinant enzymes." Adelsberger H., Hertel C., Glawischnig E., Zverlov V.V., Schwarz W.H. Microbiology 150:2257-2266(2004) [PubMed: 15256568] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION, SUBCELLULAR LOCATION, BIOPHYSICOCHEMICAL PROPERTIES. Strain: NCIB 11745.
[2]	"Co-operative binding of triplicate carbohydrate-binding modules from a thermophilic xylanase." Boraston A.B., McLean B.W., Chen G., Li A., Warren R.A.J., Kilburn D.G. Mol. Microbiol. 43:187-194(2002) [PubMed: 11849546] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 235-651, FUNCTION. Strain: NCIB 11745.
[3]	"Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and 'galactose-binding' domains." Boraston A.B., Notenboom V., Warren R.A.J., Kilburn D.G., Rose D.R., Davies G. J. Mol. Biol. 327:659-669(2003) [PubMed: 12634060] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) OF 507-651 IN COMPLEX WITH SUBSTRATE AND CALCIUM IONS.
[4]	"Binding sub-site dissection of a family 6 carbohydrate-binding module by X-ray crystallography and isothermal titration." Van Bueren A.L., Boraston A.B. Submitted (JUN-2004) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 235-373 IN COMPLEX WITH SUBSTRATE AND CALCIUM IONS.

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Cross-references

Sequence databases

AJ508403 Genomic DNA. Translation: CAD48307.1.
AF417638 Genomic DNA. Translation: AAL14106.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NAE	X-ray	2.05	A	507-651	[»]
1O8P	X-ray	2.00	A	507-651	[»]
1O8S	X-ray	1.15	A	507-651	[»]
1OD3	X-ray	1.00	A	507-651	[»]
1UY1	X-ray	1.80	A	233-373	[»]
1UY2	X-ray	1.70	A	233-373	[»]
1UY3	X-ray	1.89	A	233-373	[»]
1UY4	X-ray	1.69	A	233-373	[»]

SMR

Q8GJ44. Positions 382-509.

ModBase

Search...

Family and domain databases

InterPro

IPR005084. CBM_6.
IPR006584. Cellulose_bd_IV.
IPR001137. Glyco_hydro_11.
IPR013319. Glyco_hydro_11/12_cat.
[Graphical view]

Gene3D

G3DSA:2.60.120.180. Glyco_hydro_11/12_cat. 1 hit.

Pfam

PF03422. CBM_6. 3 hits.
PF00457. Glyco_hydro_11. 1 hit.
[Graphical view]

SMART

SM00606. CBD_IV. 3 hits.
[Graphical view]

PROSITE

PS51175. CBM6. 3 hits.
PS00776. GLYCOSYL_HYDROL_F11_1. 1 hit.
PS00777. GLYCOSYL_HYDROL_F11_2. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

XYNA1_CLOSR

Accession

Primary (citable) accession number: Q8GJ44
Secondary accession number(s): Q93AQ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2006
Last sequence update:	May 30, 2006
Last modified:	November 25, 2008
This is version 38 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Keywords

Gene Ontology (GO)

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Family and domain databases

Entry information

Relevant documents