P24300 (XYLA_STRRU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Xylose isomerase
EC=5.3.1.5

Gene names

Name:

xylA

Organism

Streptomyces rubiginosus

Taxonomic identifier

1929 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Streptomycineae › Streptomycetaceae › Streptomyces

Protein attributes

Sequence length	388 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	Involved in D-xylose catabolism. HAMAP-Rule MF_00455
Catalytic activity	D-xylose = D-xylulose. HAMAP-Rule MF_00455
Cofactor	Binds 2 magnesium ions per subunit By similarity.
Subunit structure	Homotetramer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00455.
Sequence similarities	Belongs to the xylose isomerase family.
Caution	According to the crystallographic study residue 40 could be Gln.

Ontologies

Keywords
Biological process	Carbohydrate metabolism Pentose shunt Xylose metabolism
Cellular component	Cytoplasm
Ligand	Magnesium Metal-binding
Molecular function	Isomerase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	D-xylose metabolic process Inferred from electronic annotation. Source: HAMAP pentose-phosphate shunt Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	magnesium ion binding Inferred from electronic annotation. Source: HAMAP xylose isomerase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed HAMAP-Rule MF_00455

Chain

2 – 388

387

Xylose isomerase HAMAP-Rule MF_00455

PRO_0000195805

Sites

Active site

54

1

Active site

57

1

By similarity

Metal binding

181

1

Magnesium 1

Metal binding

217

1

Magnesium 1

Metal binding

217

1

Magnesium 2

Metal binding

220

1

Magnesium 2

Metal binding

245

1

Magnesium 1

Metal binding

255

1

Magnesium 2

Metal binding

257

1

Magnesium 2

Metal binding

287

1

Magnesium 1

Secondary structure

1

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388

Helix Strand Turn

Details...

Helix

7 – 9

3

Beta strand

11 – 14

4

Helix

15 – 18

4

Helix

36 – 45

10

Beta strand

50 – 54

5

Helix

55 – 58

4

Helix

65 – 82

18

Beta strand

88 – 90

3

Beta strand

94 – 96

3

Helix

97 – 99

3

Beta strand

103 – 105

3

Helix

109 – 128

20

Beta strand

132 – 136

5

Beta strand

142 – 145

4

Helix

146 – 148

3

Helix

151 – 172

22

Beta strand

177 – 180

4

Beta strand

184 – 193

10

Helix

196 – 203

8

Beta strand

206 – 208

3

Helix

209 – 211

3

Beta strand

212 – 214

3

Helix

218 – 222

5

Turn

223 – 225

3

Helix

228 – 237

10

Beta strand

251 – 254

4

Helix

265 – 278

14

Beta strand

284 – 286

3

Helix

296 – 322

27

Helix

324 – 332

9

Helix

335 – 338

4

Helix

347 – 352

6

Helix

354 – 356

3

Turn

357 – 359

3

Helix

362 – 367

6

Helix

372 – 384

13

Sequences

	Sequence		Length	Mass (Da)
	P24300 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 4C675184B62C97FB	FASTA	388	43,227
	10 20 30 40 50 60 MNYQPTPEDR FTFGLWTVGW QGRDPFGDAT RRALDPVESV RRLAELGAHG VTFHDDDLIP 70 80 90 100 110 120 FGSSDSEREE HVKRFRQALD DTGMKVPMAT TNLFTHPVFK DGGFTANDRD VRRYALRKTI 130 140 150 160 170 180 RNIDLAVELG AETYVAWGGR EGAESGGAKD VRDALDRMKE AFDLLGEYVT SQGYDIRFAI 190 200 210 220 230 240 EPKPNEPRGD ILLPTVGHAL AFIERLERPE LYGVNPEVGH EQMAGLNFPH GIAQALWAGK 250 260 270 280 290 300 LFHIDLNGQN GIKYDQDLRF GAGDLRAAFW LVDLLESAGY SGPRHFDFKP PRTEDFDGVW 310 320 330 340 350 360 ASAAGCMRNY LILKERAAAF RADPEVQEAL RASRLDELAR PTAADGLQAL LDDRSAFEEF 370 380 DVDAAAARGM AFERLDQLAM DHLLGARG

References

[1]	"Genetic organization and regulation of the xylose degradation genes in Streptomyces rubiginosus." Wong H.C., Ting Y., Lin H.C., Reichert F., Myambo K., Watt K.W., Toy P.L., Drummond R.J. J. Bacteriol. 173:6849-6858(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator." Carrell H.L., Glusker J.P., Burger V., Manfre F., Tritsch D., Biellmann J.-F. Proc. Natl. Acad. Sci. U.S.A. 86:4440-4444(1989) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[3]	"A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose." Whitlow M., Howard A.J., Finzel B.C., Poulos T.L., Winborne E., Gilliland G.L. Proteins 9:153-173(1991) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M73789 Genomic DNA. Translation: AAA26838.1.

PIR

B41339.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GW9	X-ray	1.55	A	1-387	[»]
1MNZ	X-ray	0.99	A	1-388	[»]
1O1H	X-ray	1.40	A/B	2-387	[»]
1OAD	X-ray	1.50	A/B	2-388	[»]
1XIB	X-ray	1.60	A	2-387	[»]
1XIC	X-ray	1.60	A	2-387	[»]
1XID	X-ray	1.70	A	2-387	[»]
1XIE	X-ray	1.70	A	2-387	[»]
1XIF	X-ray	1.60	A	2-387	[»]
1XIG	X-ray	1.70	A	2-387	[»]
1XIH	X-ray	1.70	A	2-387	[»]
1XII	X-ray	1.70	A	2-387	[»]
1XIJ	X-ray	1.70	A	2-387	[»]
1XIS	X-ray	1.60	A	2-388	[»]
2G4J	X-ray	1.85	A	2-387	[»]
2GLK	X-ray	0.94	A	2-387	[»]
2GUB	X-ray	1.80	A	2-387	[»]
2GVE	neutron diffraction	2.20	A	2-387	[»]
2XIS	X-ray	1.71	A	2-388	[»]
3CWH	neutron diffraction	2.20	A	1-388	[»]
3GNX	X-ray	2.00	A/E	2-388	[»]
3KBJ	X-ray	2.00	A	1-388	[»]
3KBM	X-ray	2.00	A	1-388	[»]
3KBN	X-ray	1.53	A	1-388	[»]
3KBS	X-ray	1.80	A	1-388	[»]
3KBV	X-ray	1.80	A	1-388	[»]
3KBW	X-ray	1.60	A	1-388	[»]
3KCJ	Other	1.80	A	1-388	[»]
3KCL	Other	2.00	A	1-388	[»]
3KCO	Other	1.80	A	1-388	[»]
3N4A	X-ray	1.94	A	2-388	[»]
3QYS	X-ray	1.85	A	1-388	[»]
3QZA	Other	2.00	A	1-388	[»]
3U3H	X-ray	0.97	A	1-388	[»]
3XIS	X-ray	1.60	A	2-388	[»]
4A8I	X-ray	0.95	A	1-388	[»]
4A8L	X-ray	1.35	A	1-388	[»]
4A8N	X-ray	1.20	A	1-388	[»]
4A8R	X-ray	1.42	A	1-388	[»]
4DUO	X-ray	2.00	A	1-388	[»]
4DVO	Other	2.00	A	1-388	[»]
4E3V	X-ray	1.50	A	1-388	[»]
4XIS	X-ray	1.60	A	2-388	[»]
8XIA	X-ray	1.90	A	1-388	[»]
9XIA	X-ray	1.90	A	1-388	[»]

ProteinModelPortal

P24300.

SMR

P24300. Positions 1-388.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-58982N.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.20.20.150. 1 hit.

HAMAP

MF_00455. Xylose_isom_A.

InterPro

IPR013022. Xyl_isomerase-like_TIM-brl.
IPR013453. XylA_actinobac.
IPR001998. Xylose_isomerase.
[Graphical view]

Pfam

PF01261. AP_endonuc_2. 1 hit.
[Graphical view]

PRINTS

PR00688. XYLOSISMRASE.

SUPFAM

SSF51658. Xyl_isomerase-like_TIM-brl. 1 hit.

TIGRFAMs

TIGR02631. xylA_Arthro. 1 hit.

PROSITE

PS51415. XYLOSE_ISOMERASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00126. Vitamin C.

EvolutionaryTrace

P24300.

Entry information

Entry name

XYLA_STRRU

Accession

Primary (citable) accession number: P24300

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 102 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program