C6CRV0 (XYNA1_PAESJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Endo-1,4-beta-xylanase A
EC=3.2.1.8

Alternative name(s):
1,4-beta-D-xylan xylanohydrolase A

Gene names

Name:	xynA1
Synonyms:	xynA
Ordered Locus Names:	Pjdr2_0221

Organism

Paenibacillus sp. (strain JDR-2) [Complete proteome] [HAMAP]

Taxonomic identifier

324057 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Paenibacillaceae › Paenibacillus

Protein attributes

Sequence length	1462 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the depolymerization of methylglucuronoxylan (MeGAXn), a beta-1,4 xylan in which 10% to 20% of the xylose residues are substituted with alpha-1,2-4-O-methylglucuronate (MeGA) residues, which is predominant in hemicellulose fractions of hardwood and crop residues. Generates xylobiose (X2) and aldotetrauronate (MeGAX3) as the predominant products of MeGAXn hydrolysis; these products are then directly assimilated by the bacterium for subsequent metabolism. Thus, allows the bacterium to efficiently use polymeric MeGAXn as a growth substrate. Ref.1
Catalytic activity	Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans. Ref.1
Pathway	Glycan degradation; xylan degradation.
Subcellular location	Secreted › cell wall Ref.1.
Sequence similarities	Belongs to the glycosyl hydrolase 10 (cellulase F) family. Contains 3 CBM-cenC (cenC-type cellulose-binding) domains. Contains 3 SLH (S-layer homology) domains.
Biophysicochemical properties	Kinetic parameters: Vmax=8.0 µmol/min/mg enzyme with sweet gum methylglucuronoxylan as substrate Ref.1 pH dependence: Optimum pH is 6.5 with sweet gum methylglucuronoxylan as substrate. Temperature dependence: Optimum temperature is 45 degrees Celsius with sweet gum methylglucuronoxylan as substrate.

Ontologies

Keywords
Biological process	Carbohydrate metabolism Polysaccharide degradation Xylan degradation
Cellular component	Cell wall Secreted
Domain	Repeat Signal
Molecular function	Glycosidase Hydrolase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	xylan catabolic process Inferred from direct assay Ref.1. Source: UniProtKB
Cellular_component	cell wall Inferred from direct assay Ref.1. Source: UniProtKB extracellular region Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	carbohydrate binding Inferred from electronic annotation. Source: InterPro endo-1,4-beta-xylanase activity Inferred from direct assay Ref.1. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 30

30

Potential

Chain

31 – 1462

1432

Endo-1,4-beta-xylanase A

PRO_5000484609

Regions

Domain

64 – 165

102

CBM-cenC 1

Domain

207 – 319

113

CBM-cenC 2

Domain

360 – 490

131

CBM-cenC 3

Domain

1279 – 1342

64

SLH 1

Domain

1345 – 1404

60

SLH 2

Domain

1407 – 1462

56

SLH 3

Compositional bias

186 – 191

6

Poly-Thr

Sites

Active site

651

1

Proton donor By similarity

Active site

706

1

By similarity

Active site

775

1

Nucleophile By similarity

Experimental info

Sequence conflict

313

1

S → T in CAI79477. Ref.1

Sequence conflict

454 – 461

8

SLASKTIT → TPTTQAWQARRLP in CAI79477. Ref.1

Secondary structure

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1462

Helix Strand Turn

Details...

Helix

520 – 523

4

Turn

524 – 527

4

Beta strand

529 – 534

6

Helix

536 – 539

4

Helix

541 – 550

10

Beta strand

552 – 558

7

Helix

562 – 565

4

Helix

575 – 586

12

Beta strand

590 – 597

8

Beta strand

599 – 601

3

Helix

604 – 606

3

Beta strand

608 – 610

3

Beta strand

616 – 618

3

Helix

621 – 639

19

Helix

640 – 642

3

Beta strand

643 – 650

8

Helix

664 – 666

3

Helix

671 – 676

6

Helix

680 – 694

15

Beta strand

701 – 707

7

Helix

712 – 732

21

Turn

733 – 735

3

Beta strand

741 – 744

4

Beta strand

747 – 749

3

Helix

754 – 765

12

Turn

766 – 768

3

Beta strand

770 – 779

10

Helix

787 – 807

21

Helix

808 – 811

4

Beta strand

812 – 817

6

Helix

822 – 824

3

Helix

828 – 830

3

Beta strand

833 – 835

3

Helix

843 – 849

7

Sequences

	Sequence		Length	Mass (Da)
	C6CRV0 [UniParc]. Last modified September 1, 2009. Version 1. Checksum: AE29664CDEA3BF3E	FASTA	1,462	157,322
	10 20 30 40 50 60 MSRSLKKFVS ILLAAALLIP IGRLAPVAEA AENPTIVYHE DFAIDKGKAI QSGGASLTQV 70 80 90 100 110 120 TGKVFDGNND GSALYVSNRA NTWDAADFKF ADIGLQNGKT YTVTVKGYVD QDATVPSGAQ 130 140 150 160 170 180 AFLQAVDSNN YGFLASANFA AGTAFTLTKE FTVDTSVSTQ LRVQSSEEGK AVPFYIGDIL 190 200 210 220 230 240 ITANPTTTTN TVYHEDFATD KGKAVQSGGA NLAQVADKVF DGNDDGKALY VSNRANTWDA 250 260 270 280 290 300 ADFKFADIGL QNGKTYTVTV KGYVDQDATV PSGAQAFLQA VDSNNYGFLA SANFAARSAF 310 320 330 340 350 360 TLTKEFTVDT SVSTQLRVQS SEEGKAVPFY IGDILITETV NSGGGQEDPP RPPALPFNTI 370 380 390 400 410 420 TFEDQTAGGF TGRAGTETLT VTNESNHTAD GSYSLKVEGR TTSWHGPSLR VEKYVDKGYE 430 440 450 460 470 480 YKVTAWVKLL SPETSTKLEL ASQVGDGGSA NYPSLASKTI TAADGWVQLQ GNYRYNSVGG 490 500 510 520 530 540 EYLTIYVQSS NATASYYIDD ISFESTGSGP VGIQKDLAPL KDVYKNDFLI GNAISAEDLE 550 560 570 580 590 600 GTRLELLKMH HDVVTAGNAM KPDALQPTKG NFTFTAADAM IDKVLAEGMK MHGHVLVWHQ 610 620 630 640 650 660 QSPAWLNTKK DDNNNTVPLG RDEALDNLRT HIQTVMKHFG NKVISWDVVN EAMNDNPSNP 670 680 690 700 710 720 ADYKASLRQT PWYQAIGSDY VEQAFLAARE VLDENPSWNI KLYYNDYNED NQNKATAIYN 730 740 750 760 770 780 MVKDINDRYA AAHNGKLLID GVGMQGHYNI NTNPDNVKLS LEKFISLGVE VSVSELDVTA 790 800 810 820 830 840 GNNYTLPENL AVGQAYLYAQ LFKLYKEHAD HIARVTFWGM DDNTSWRAEN NPLLFDKNLQ 850 860 870 880 890 900 AKPAYYGVID PDKYMEEHAP ESKDANQAEA QYGTPVIDGT VDSIWSNAQA MPVNRYQMAW 910 920 930 940 950 960 QGATGTAKAL WDDQNLYVLI QVSDSQLNKA NENAWEQDSV EVFLDQNNGK TTFYQNDDGQ 970 980 990 1000 1010 1020 YRVNFDNETS FSPASIAAGF ESQTKKTANS YTVELKIPLT AVTPANQKKL GFDVQINDAT 1030 1040 1050 1060 1070 1080 DGARTSVAAW NDTTGNGYQD TSVYGELTLA GKGTGGTGTV GTTVPQTGNV VKNPDGSTTL 1090 1100 1110 1120 1130 1140 KPEVKTTNGN AVGTVTGDDL KKALDQAAPA AGGKKQVIID VPLQANAATY AVQLPTQSLK 1150 1160 1170 1180 1190 1200 SQDGYQLTAK IANAFIQIPS NMLANTNVTT DQVSIRVAKA SLDNVDAATR ELIGNRPVID 1210 1220 1230 1240 1250 1260 LSLVAGGNVI AWNNPTAPVT VAVPYAPTAE ELKHPEHILI WYIDGSGKAT PVPNSRYDAA 1270 1280 1290 1300 1310 1320 LGAVVFQTTH FSTYAAVSVF TTFGDLAKVP WAKEAIDAMA SRGVIKGTGE NTFSPAASIK 1330 1340 1350 1360 1370 1380 RADFIALLVR ALELHGTGTT DTAMFSDVPA NAYYYNELAV AKQLGIATGF EDNTFKPDSS 1390 1400 1410 1420 1430 1440 ISRQDMMVLT TRALAVLGKQ LPAGGSLNAF SDAASVAGYA QDSVAALVKA GVVQGSGSKL 1450 1460 APNDQLTRAE AAVILYRIWK LQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization." Stjohn F.J., Rice J.D., Preston J.F. Appl. Environ. Microbiol. 72:1496-1506(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION. Strain: JDR-2.
[2]	"Complete genome sequence of Paenibacillus sp. strain JDR-2." Chow V., Nong G., St John F.J., Rice J.D., Dickstein E., Chertkov O., Bruce D., Detter C., Brettin T., Han J., Woyke T., Pitluck S., Nolan M., Pati A., Martin J., Copeland A., Land M.L., Goodwin L. , Jones J.B., Ingram L.O., Shanmugam K.T., Preston J.F. Stand. Genomic Sci. 6:1-10(2012) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: JDR-2.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ938162 Genomic DNA. Translation: CAI79477.1.
CP001656 Genomic DNA. Translation: ACS98901.1.

RefSeq

YP_003008988.1. NC_012914.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3RDK	X-ray	1.49	A/B	518-851	[»]
3RO8	X-ray	1.34	A/B/C/D/E/F/G/H	518-851	[»]
4E4P	X-ray	1.92	A/B	518-851	[»]

ProteinModelPortal

C6CRV0.

ModBase

Search...

Protein-protein interaction databases

STRING

324057.Pjdr2_0221.

Protein family/group databases

CAZy

CBM22. Carbohydrate-Binding Module Family 22.
CBM9. Carbohydrate-Binding Module Family 9.
GH10. Glycoside Hydrolase Family 10.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ACS98901; ACS98901; Pjdr2_0221.

GeneID

8127565.

KEGG

pjd:Pjdr2_0221.

PATRIC

22830917. VBIPaeSp118865_0225.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG3693.

HOGENOM

HOG000049670.

KO

K01181.

OMA

RANTWDA.

ProtClustDB

CLSK2482236.

Enzyme and pathway databases

BioCyc

PSP324057:GH5H-261-MONOMER.

UniPathway

UPA00114.

Family and domain databases

Gene3D

2.60.120.260. 3 hits.
2.60.40.1190. 1 hit.
3.20.20.80. 1 hit.

InterPro

IPR010502. Carb-bd_dom_fam9.
IPR008960. Carb-bd_dom_fam9-like.
IPR015922. Carb-bd_dom_fam9-like_subgr.
IPR003305. CenC_carb-bd.
IPR008979. Galactose-bd-like.
IPR001000. Glyco_hydro_10.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
IPR001119. S-layer_homology_dom.
[Graphical view]

Pfam

PF02018. CBM_4_9. 3 hits.
PF06452. DUF1083. 1 hit.
PF00331. Glyco_hydro_10. 1 hit.
PF00395. SLH. 3 hits.
[Graphical view]

PRINTS

PR00134. GLHYDRLASE10.

SMART

SM00633. Glyco_10. 1 hit.
[Graphical view]

SUPFAM

SSF49344. CBD9-like. 1 hit.
SSF49785. Gal_bind_like. 3 hits.
SSF51445. Glyco_hydro_cat. 1 hit.

PROSITE

PS00591. GLYCOSYL_HYDROL_F10. 1 hit.
PS51272. SLH. 3 hits.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

XYNA1_PAESJ

Accession

Primary (citable) accession number: C6CRV0
Secondary accession number(s): Q53I45

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 31, 2011
Last sequence update:	September 1, 2009
Last modified:	May 29, 2013
This is version 33 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program