Reviewed, UniProtKB/Swiss-Prot P00489 (PYGM_RABIT)

Names and origin

Protein names

Recommended name:
    Glycogen phosphorylase, muscle form
    EC=2.4.1.1
Alternative name(s):
    Myophosphorylase

Gene names

Name:

PYGM

Organism

Oryctolagus cuniculus (Rabbit)

Taxonomic identifier

9986 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Lagomorpha › Leporidae › Oryctolagus

Protein attributes

Sequence length	843 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	Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
Catalytic activity	(1,4-alpha-D-glucosyl)(n) + phosphate = (1,4-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate.
Cofactor	Pyridoxal phosphate.
Enzyme regulation	Activity of phosphorylase is controlled both by allosteric means (through the noncovalent binding of metabolites) and by covalent modification. Thus AMP allosterically activates, whereas ATP, ADP, and glucose-6-phosphate allosterically inhibit, phosphorylase B.
Subunit structure	Homodimer. Dimers associate into a tetramer to form the enzymatically active phosphorylase A.
Post-translational modification	Phosphorylation of Ser-15 converts phosphorylase B (unphosphorylated) to phosphorylase A.
Sequence similarities	Belongs to the glycogen phosphorylase family.

Ontologies

Keywords
Biological process	Carbohydrate metabolism Glycogen metabolism
Ligand	Nucleotide-binding Pyridoxal phosphate
Molecular function	Glycosyltransferase Transferase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Allosteric enzyme Direct protein sequencing
Gene Ontology (GO)
Biological process	glycogen metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorylase activity Inferred from electronic annotation. Source: EC pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.2

Chain

2 – 843

842

Glycogen phosphorylase, muscle form

PRO_0000188532

Sites

Binding site

76

1

AMP

Site

109

1

Involved in the association of subunits

Site

143

1

Involved in the association of subunits

Site

156

1

Can be labeled by an AMP analog; may be involved in allosteric regulation

Amino acid modifications

Modified residue

2

1

N-acetylserine Ref.1

Modified residue

15

1

Phosphoserine; by PHK; in form phosphorylase A Ref.2

Modified residue

473

1

Phosphotyrosine By similarity

Modified residue

681

1

N6-(pyridoxal phosphate)lysine

Experimental info

Sequence conflict

31 – 33

3

NFN → DFD AA sequence Ref.2

Sequence conflict

43

1

D → N AA sequence Ref.2

Sequence conflict

56 – 58

3

LAH → HAL AA sequence Ref.2

Sequence conflict

89

1

E → Q AA sequence Ref.2

Sequence conflict

113

1

T → D AA sequence Ref.2

Sequence conflict

309

1

Missing AA sequence Ref.2

Sequence conflict

578 – 579

2

LL → FF in CAA26833. Ref.6

Sequence conflict

610

1

A → P in BAA00027. Ref.1

Sequence conflict

610

1

A → P in CAA27816. Ref.1

Sequence conflict

713

1

G → C in CAA26833. Ref.6

Secondary structure

1

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843

Helix Strand Turn

Details...

Helix

9 – 13

5

Helix

15 – 17

3

Helix

22 – 38

17

Turn

44 – 46

3

Helix

49 – 78

30

Beta strand

82 – 86

5

Beta strand

90 – 93

4

Helix

96 – 102

7

Helix

106 – 115

10

Helix

120 – 124

5

Beta strand

130 – 133

4

Helix

136 – 150

15

Beta strand

155 – 160

6

Beta strand

168 – 172

5

Beta strand

175 – 179

5

Turn

183 – 186

4

Helix

195 – 197

3

Beta strand

199 – 204

6

Beta strand

206 – 210

5

Beta strand

213 – 218

6

Beta strand

220 – 232

13

Beta strand

234 – 236

3

Beta strand

239 – 248

10

Helix

263 – 268

6

Helix

270 – 274

5

Helix

275 – 277

3

Helix

291 – 313

23

Helix

325 – 328

4

Helix

330 – 333

4

Beta strand

334 – 341

8

Turn

342 – 345

4

Helix

346 – 356

11

Helix

362 – 372

11

Beta strand

373 – 376

4

Helix

382 – 384

3

Beta strand

387 – 389

3

Helix

390 – 396

7

Helix

398 – 418

21

Helix

423 – 429

7

Beta strand

431 – 433

3

Beta strand

435 – 437

3

Beta strand

439 – 441

3

Helix

442 – 448

7

Beta strand

451 – 457

7

Helix

458 – 466

9

Turn

467 – 469

3

Helix

470 – 475

6

Helix

477 – 479

3

Beta strand

480 – 482

3

Helix

490 – 495

6

Helix

498 – 508

11

Helix

511 – 514

4

Helix

516 – 525

10

Helix

529 – 554

26

Beta strand

560 – 569

10

Helix

573 – 575

3

Helix

577 – 593

17

Beta strand

602 – 607

6

Helix

615 – 631

17

Turn

635 – 639

5

Beta strand

640 – 646

7

Helix

651 – 657

7

Helix

658 – 660

3

Beta strand

662 – 666

5

Helix

678 – 684

7

Beta strand

688 – 691

4

Helix

697 – 704

8

Helix

706 – 708

3

Beta strand

709 – 711

3

Helix

716 – 725

10

Helix

729 – 735

7

Helix

737 – 747

11

Turn

748 – 751

4

Turn

756 – 759

4

Helix

760 – 768

9

Helix

774 – 777

4

Helix

778 – 792

15

Helix

795 – 806

12

Helix

810 – 812

3

Helix

814 – 824

11

Sequences

	Sequence		Length	Mass (Da)
	P00489-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 9884F06FDD3AE9D3	FASTA	843	97,289
	10 20 30 40 50 60 MSRPLSDQEK RKQISVRGLA GVENVTELKK NFNRHLHFTL VKDRNVATPR DYYFALAHTV 70 80 90 100 110 120 RDHLVGRWIR TQQHYYEKDP KRIYYLSLEF YMGRTLQNTM VNLALENACD EATYQLGLDM 130 140 150 160 170 180 EELEEIEEDA GLGNGGLGRL AACFLDSMAT LGLAAYGYGI RYEFGIFNQK ICGGWQMEEA 190 200 210 220 230 240 DDWLRYGNPW EKARPEFTLP VHFYGRVEHT SQGAKWVDTQ VVLAMPYDTP VPGYRNNVVN 250 260 270 280 290 300 TMRLWSAKAP NDFNLKDFNV GGYIQAVLDR NLAENISRVL YPNDNFFEGK ELRLKQEYFV 310 320 330 340 350 360 VAATLQDIIR RFKSSKFGCR DPVRTNFDAF PDKVAIQLND THPSLAIPEL MRVLVDLERL 370 380 390 400 410 420 DWDKAWEVTV KTCAYTNHTV LPEALERWPV HLLETLLPRH LQIIYEINQR FLNRVAAAFP 430 440 450 460 470 480 GDVDRLRRMS LVEEGAVKRI NMAHLCIAGS HAVNGVARIH SEILKKTIFK DFYELEPHKF 490 500 510 520 530 540 QNKTNGITPR RWLVLCNPGL AEIIAERIGE EYISDLDQLR KLLSYVDDEA FIRDVAKVKQ 550 560 570 580 590 600 ENKLKFAAYL EREYKVHINP NSLFDVQVKR IHEYKRQLLN CLHVITLYNR IKKEPNKFVV 610 620 630 640 650 660 PRTVMIGGKA APGYHMAKMI IKLITAIGDV VNHDPVVGDR LRVIFLENYR VSLAEKVIPA 670 680 690 700 710 720 ADLSEQISTA GTEASGTGNM KFMLNGALTI GTMDGANVEM AEEAGEENFF IFGMRVEDVD 730 740 750 760 770 780 RLDQRGYNAQ EYYDRIPELR QIIEQLSSGF FSPKQPDLFK DIVNMLMHHD RFKVFADYEE 790 800 810 820 830 840 YVKCQERVSA LYKNPREWTR MVIRNIATSG KFSSDRTIAQ YAREIWGVEP SRQRLPAPDE KIP

References

[1]	"Complete cDNA sequence for rabbit muscle glycogen phosphorylase." Nakano K., Hwang P.K., Fletterick R.J. FEBS Lett. 204:283-287(1986) [PubMed: 3015680] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Sequence of the amino-terminal 349 residues of rabbit muscle glycogen phosphorylase including the sites of covalent and allosteric control." Koide A., Titani K., Ericsson L.H., Kumar S., Neurath H., Walsh K.A. Biochemistry 17:5657-5672(1978) [PubMed: 728424] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-351.
[3]	"Amino acid sequence of two cyanogen bromide fragments of glycogen phosphorylase." Hermann J., Titani K., Ericsson L.H., Wade R.D., Neurath H., Walsh K.A. Biochemistry 17:5672-5679(1978) [PubMed: 728425] [Abstract] Cited for: PROTEIN SEQUENCE OF 352-429 AND 443-605.
[4]	"Sequence of the carboxyl-terminal 492 residues of rabbit muscle glycogen phosphorylase including the pyridoxal 5'-phosphate binding site." Titani K., Koide A., Ericsson L.H., Kumar S., Hermann J., Wade R.D., Walsh K.A., Neurath H., Fischer E.H. Biochemistry 17:5680-5693(1978) [PubMed: 728426] [Abstract] Cited for: PROTEIN SEQUENCE OF 352-843.
[5]	"Inactivation of phosphorylase b by potassium ferrate. Identification of a tyrosine residue involved in the binding of adenosine 5'-monophosphate." Lee Y.M., Benisek W.F. J. Biol. Chem. 253:5460-5463(1978) [PubMed: 670209] [Abstract] Cited for: PROTEIN SEQUENCE OF 71-81.
[6]	"Comparative sequence analysis of rat, rabbit, and human muscle glycogen phosphorylase cDNAs." Hwang P.K., See Y.P., Vincentini A.M., Powers M.A., Fletterick R.J., Crerar M.M. Eur. J. Biochem. 152:267-274(1985) [PubMed: 3840433] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 575-843.
[7]	"Crystallographic analysis of phosphorylase alpha at 2.5-A resolution, a comment on the chemical sequence." Sprang S.R., Fletterick R.J. Biochemistry 17:5693-5694(1978) [PubMed: 728427] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF PHOSPHORYLASE A.
[8]	"Domain separation in the activation of glycogen phosphorylase a." Goldsmith E.J., Sprang S.R., Hamlin R., Xuong N.-H., Fletterick R.J. Science 245:528-532(1989) [PubMed: 2756432] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF PHOSPHORYLASE A.
[9]	"Structure of the nucleotide activation switch in glycogen phosphorylase a." Sprang S.R., Goldsmith E.J., Fletterick R.J. Science 237:1012-1019(1987) [PubMed: 3616621] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF PHOSPHORYLASE A WITH AMP.
[10]	"Assignment of the amino acid sequence to the crystal structure of glycogen phosphorylase b." Jenkins J.A., Johnson L.N., Wilson K.S. Biochemistry 17:5694-5695(1978) [PubMed: 728428] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF PHOSPHORYLASE B.
[11]	"The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies." Oikonomakos N.G., Zographos S.E., Johnson L.N., Papageorgiou A.C., Acharya K.R. J. Mol. Biol. 254:900-917(1995) [PubMed: 7500360] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF PHOSPHORYLASE B.
[12]	"Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal." Oikonomakos N.G., Zographos S.E., Tsitsanou K.E., Johnson L.N., Acharya K.R. Protein Sci. 5:2416-2428(1996) [PubMed: 8976550] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF PHOSPHORYLASE B.
[13]	"The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8-A resolution and 100 K: the role of the water structure and its contribution to binding." Gregoriou M., Noble M.E.M., Watson K.A., Garman E.F., Krulle T.M., de la Fuente C., Fleet G.W., Oikonomakos N.G., Johnson L.N. Protein Sci. 7:915-927(1998) [PubMed: 9568898] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF PHOSPHORYLASE B.
+	Additional computationally mapped references.

Web resources

ProZyme technical fact sheet

Cross-references

Sequence databases

EMBLGenBankDDBJ

D00040 mRNA. Translation: BAA00027.1.
X04265 mRNA. Translation: CAA27816.1.
X03030 mRNA. Translation: CAA26833.1.

PIR

PHRBG. A24302.

RefSeq

NP_001075653.1.

UniGene

Ocu.2087

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A8I	X-ray	1.78	A	1-843	[»]
1ABB	X-ray	2.80	A/B/C/D	11-838	[»]
1AXR	X-ray	2.30	A	1-843	[»]
1B4D	X-ray	2.00	A	1-843	[»]
1BX3	X-ray	2.30	A	1-843	[»]
1C50	X-ray	2.30	A	14-843	[»]
1C8K	X-ray	1.76	A	1-843	[»]
1C8L	X-ray	2.30	A	1-843	[»]
1E1Y	X-ray	2.23	A	1-843	[»]
1FS4	X-ray	2.38	A	1-843	[»]
1FTQ	X-ray	2.35	A	1-843	[»]
1FTW	X-ray	2.36	A	1-843	[»]
1FTY	X-ray	2.38	A	1-843	[»]
1FU4	X-ray	2.36	A	1-843	[»]
1FU7	X-ray	2.36	A	1-843	[»]
1FU8	X-ray	2.35	A	1-843	[»]
1GFZ	X-ray	2.30	A	1-843	[»]
1GG8	X-ray	2.31	A	1-843	[»]
1GGN	X-ray	2.36	A	1-843	[»]
1GPA	X-ray	2.90	A/B/C/D	1-843	[»]
1GPB	X-ray	1.90	A	1-843	[»]
1GPY	X-ray	2.40	A	1-843	[»]
1H5U	X-ray	1.76	A	1-843	[»]
1HLF	X-ray	2.26	A	1-843	[»]
1K06	X-ray	1.80	A	1-843	[»]
1K08	X-ray	2.26	A	1-843	[»]
1KTI	X-ray	1.97	A	1-843	[»]
1LWN	X-ray	2.00	A	1-843	[»]
1LWO	X-ray	2.00	A	1-843	[»]
1NOI	X-ray	2.50	A/B/C/D	2-843	[»]
1NOJ	X-ray	2.40	A	1-843	[»]
1NOK	X-ray	2.40	A	1-843	[»]
1P29	X-ray	2.20	A	1-843	[»]
1P2B	X-ray	2.20	A	1-843	[»]
1P2D	X-ray	1.94	A	1-843	[»]
1P2G	X-ray	2.30	A	1-843	[»]
1P4G	X-ray	2.10	A	1-843	[»]
1P4H	X-ray	2.06	A	1-843	[»]
1P4J	X-ray	2.00	A	1-843	[»]
1PYG	X-ray	2.87	A/B/C/D	1-843	[»]
1UZU	X-ray	2.30	A	1-843	[»]
1WUT	X-ray	2.26	A	1-843	[»]
1WUY	X-ray	2.26	A	1-843	[»]
1WV0	X-ray	2.26	A	1-843	[»]
1WV1	X-ray	2.26	A	1-843	[»]
1WW2	X-ray	1.90	A	1-843	[»]
1WW3	X-ray	1.80	A	1-843	[»]
1XC7	X-ray	1.83	A	1-843	[»]
1XKX	X-ray	1.93	A	1-843	[»]
1XL0	X-ray	1.92	A	1-843	[»]
1XL1	X-ray	2.10	A	1-843	[»]
1Z62	X-ray	1.90	A	1-843	[»]
1Z6P	X-ray	2.40	A	1-843	[»]
1Z6Q	X-ray	2.03	A	1-843	[»]
2AMV	X-ray	2.30	A	1-843	[»]
2F3P	X-ray	1.94	A	2-843	[»]
2F3Q	X-ray	1.96	A	2-843	[»]
2F3S	X-ray	1.96	A	2-843	[»]
2F3U	X-ray	1.93	A	1-843	[»]
2FET	X-ray	2.03	A	2-843	[»]
2FF5	X-ray	2.03	A	2-843	[»]
2FFR	X-ray	2.03	A	13-837	[»]
2G9Q	X-ray	2.50	A	2-843	[»]
2G9R	X-ray	2.07	A	2-843	[»]
2G9U	X-ray	2.15	A	2-843	[»]
2G9V	X-ray	2.15	A	2-843	[»]
2GJ4	X-ray	1.60	A	13-836	[»]
2GM9	X-ray	2.30	A	13-837	[»]
2GPA	X-ray	2.00	A	1-843	[»]
2GPB	X-ray	2.30	A	1-843	[»]
2GPN	X-ray	1.99	A	1-843	[»]
2IEG	X-ray	1.90	A/B	2-843	[»]
2IEI	X-ray	1.91	A/B	2-843	[»]
2OFF	X-ray	2.20	A	2-843	[»]
2PRI	X-ray	2.30	A	1-843	[»]
2PRJ	X-ray	2.30	A	1-843	[»]
2PYD	X-ray	1.93	A	1-843	[»]
2PYI	X-ray	1.88	A	1-843	[»]
2QLM	X-ray	2.10	A	2-843	[»]
2QLN	X-ray	2.15	A	2-843	[»]
2QN1	X-ray	2.40	A	2-843	[»]
2QN2	X-ray	2.70	A	2-843	[»]
2QN3	X-ray	1.96	A	2-843	[»]
2QN7	X-ray	1.83	A	2-843	[»]
2QN8	X-ray	1.90	A	2-843	[»]
2QN9	X-ray	2.00	A	2-843	[»]
2QNB	X-ray	1.80	A	2-843	[»]
2QRG	X-ray	1.85	A	2-843	[»]
2QRH	X-ray	1.83	A	2-843	[»]
2QRM	X-ray	1.90	A	2-843	[»]
2QRP	X-ray	1.86	A	2-843	[»]
2QRQ	X-ray	1.80	A	2-843	[»]
2SKC	X-ray	2.40	A	1-843	[»]
2SKD	X-ray	2.40	A	1-843	[»]
2SKE	X-ray	2.46	A	1-843	[»]
3AMV	X-ray	2.10	A	1-843	[»]
3BCR	X-ray	2.14	A	2-843	[»]
3BCS	X-ray	2.00	A	2-843	[»]
3BCU	X-ray	2.03	A	2-843	[»]
3BD6	X-ray	2.00	A	2-843	[»]
3BD7	X-ray	1.90	A	2-843	[»]
3BD8	X-ray	2.10	A	2-843	[»]
3BDA	X-ray	2.00	A	2-843	[»]
3CUT	X-ray	2.30	A	2-843	[»]
3CUU	X-ray	2.30	A	2-843	[»]
3CUV	X-ray	1.93	A	2-843	[»]
3CUW	X-ray	2.00	A	2-843	[»]
3E3L	X-ray	2.59	A/B/C/D	2-843	[»]
3GPB	X-ray	2.30	A	1-843	[»]
4GPB	X-ray	2.30	A	1-843	[»]
5GPB	X-ray	2.30	A	1-843	[»]
6GPB	X-ray	2.86	A	1-843	[»]
7GPB	X-ray	2.90	A/B/C/D	1-843	[»]
8GPB	X-ray	2.20	A	1-843	[»]
9GPB	X-ray	2.90	A/B/C/D	1-843	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P00489. 1 interaction.

Protein family/group databases

CAZy

GT35. Glycosyltransferase Family 35.

Genome annotation databases

GeneID

100008972.

Phylogenomic databases

HOVERGEN

P00489.

Enzyme and pathway databases

BRENDA

2.4.1.1. 255.

Family and domain databases

InterPro

IPR011833. Glycg_phsphrylas.
IPR000811. Glyco_trans_35.
[Graphical view]

PANTHER

PTHR11468. Glyco_trans_35. 1 hit.

Pfam

PF00343. Phosphorylase. 1 hit.
[Graphical view]

PIRSF

PIRSF000460. Pprylas_GlgP. 1 hit.

TIGRFAMs

TIGR02093. P_ylase. 1 hit.

PROSITE

PS00102. PHOSPHORYLASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00131. Adenosine monophosphate.

Entry information

Entry name

PYGM_RABIT

Accession

Primary (citable) accession number: P00489

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 103 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)