Glycogen phosphorylase, muscle form - Oryctolagus cuniculus (Rabbit)

Preferred order of sections

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) [Reference proteome]

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 Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	glycogen catabolic process Inferred from electronic annotation. Source: Compara
Molecular_function	glycogen phosphorylase activity Inferred from electronic annotation. Source: Compara nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW 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

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

.

843

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P00489 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 9884F06FDD3AE9D3
Show »

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

« Hide

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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

EMBL
GenBank
DDBJ

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

PIR

PHRBG. A24302.

RefSeq

NP_001075653.1. NM_001082184.1.

UniGene

Ocu.2087.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A8I	X-ray	1.78	A	2-843	[»]
1ABB	X-ray	2.80	A/B/C/D	11-837	[»]
1AXR	X-ray	2.30	A	2-843	[»]
1B4D	X-ray	2.00	A	2-842	[»]
1BX3	X-ray	2.30	A	2-843	[»]
1C50	X-ray	2.30	A	14-843	[»]
1C8K	X-ray	1.76	A	2-842	[»]
1C8L	X-ray	2.30	A	2-842	[»]
1E1Y	X-ray	2.23	A	2-843	[»]
1FS4	X-ray	2.38	A	2-843	[»]
1FTQ	X-ray	2.35	A	2-843	[»]
1FTW	X-ray	2.36	A	2-842	[»]
1FTY	X-ray	2.38	A	2-843	[»]
1FU4	X-ray	2.36	A	2-843	[»]
1FU7	X-ray	2.36	A	2-843	[»]
1FU8	X-ray	2.35	A	2-842	[»]
1GFZ	X-ray	2.30	A	2-843	[»]
1GG8	X-ray	2.31	A	2-843	[»]
1GGN	X-ray	2.36	A	2-843	[»]
1GPA	X-ray	2.90	A/B/C/D	2-843	[»]
1GPB	X-ray	1.90	A	2-843	[»]
1GPY	X-ray	2.40	A	2-843	[»]
1H5U	X-ray	1.76	A	2-843	[»]
1HLF	X-ray	2.26	A	2-843	[»]
1K06	X-ray	1.80	A	2-843	[»]
1K08	X-ray	2.26	A	2-843	[»]
1KTI	X-ray	1.97	A	2-843	[»]
1LWN	X-ray	2.00	A	2-843	[»]
1LWO	X-ray	2.00	A	2-843	[»]
1NOI	X-ray	2.50	A/B/C/D	2-843	[»]
1NOJ	X-ray	2.40	A	2-843	[»]
1NOK	X-ray	2.40	A	2-843	[»]
1P29	X-ray	2.20	A	2-843	[»]
1P2B	X-ray	2.20	A	2-843	[»]
1P2D	X-ray	1.94	A	2-843	[»]
1P2G	X-ray	2.30	A	2-843	[»]
1P4G	X-ray	2.10	A	2-843	[»]
1P4H	X-ray	2.06	A	2-843	[»]
1P4J	X-ray	2.00	A	2-843	[»]
1PYG	X-ray	2.87	A/B/C/D	2-843	[»]
1UZU	X-ray	2.30	A	2-843	[»]
1WUT	X-ray	2.26	A	2-843	[»]
1WUY	X-ray	2.26	A	2-843	[»]
1WV0	X-ray	2.26	A	2-843	[»]
1WV1	X-ray	2.26	A	2-843	[»]
1WW2	X-ray	1.90	A	2-843	[»]
1WW3	X-ray	1.80	A	2-843	[»]
1XC7	X-ray	1.83	A	2-843	[»]
1XKX	X-ray	1.93	A	2-843	[»]
1XL0	X-ray	1.92	A	2-843	[»]
1XL1	X-ray	2.10	A	2-843	[»]
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	2-842	[»]
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	2-843	[»]
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	2-843	[»]
2SKE	X-ray	2.46	A	2-843	[»]
3AMV	X-ray	2.10	A	2-842	[»]
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	[»]
3E3N	X-ray	2.70	A/B/C/D/E/F/G/H	2-843	[»]
3E3O	X-ray	2.60	A/B/C/D	2-843	[»]
3EBO	X-ray	1.90	A	2-843	[»]
3EBP	X-ray	2.00	A	2-843	[»]
3G2H	X-ray	2.03	A	2-843	[»]
3G2I	X-ray	2.00	A	2-843	[»]
3G2J	X-ray	2.14	A	2-843	[»]
3G2K	X-ray	2.00	A	2-843	[»]
3G2L	X-ray	2.30	A	2-843	[»]
3G2N	X-ray	2.10	A	2-843	[»]
3GPB	X-ray	2.30	A	1-843	[»]
3L79	X-ray	1.86	A	1-843	[»]
3L7A	X-ray	1.90	A	1-843	[»]
3L7B	X-ray	2.00	A	1-843	[»]
3L7C	X-ray	1.93	A	1-843	[»]
3L7D	X-ray	2.00	A	1-843	[»]
3MQF	X-ray	1.95	A	2-843	[»]
3MRT	X-ray	1.98	A	2-843	[»]
3MRV	X-ray	1.94	A	2-843	[»]
3MRX	X-ray	1.95	A	2-843	[»]
3MS2	X-ray	2.10	A	2-843	[»]
3MS4	X-ray	2.07	A	2-843	[»]
3MS7	X-ray	1.95	A	2-843	[»]
3MSC	X-ray	1.95	A	2-843	[»]
3MT7	X-ray	2.00	A	2-843	[»]
3MT8	X-ray	2.00	A	2-843	[»]
3MT9	X-ray	2.05	A	2-843	[»]
3MTA	X-ray	2.23	A	2-843	[»]
3MTB	X-ray	1.95	A	2-843	[»]
3MTD	X-ray	2.10	A	2-843	[»]
3NC4	X-ray	2.07	A	3-843	[»]
3NP7	X-ray	2.05	A	2-843	[»]
3NP9	X-ray	2.00	A	2-843	[»]
3NPA	X-ray	1.97	A	2-843	[»]
3S0J	X-ray	2.00	A	2-843	[»]
3SYM	X-ray	2.40	A	2-843	[»]
3SYR	X-ray	2.40	A	2-843	[»]
3T3D	X-ray	2.50	A	2-843	[»]
3T3E	X-ray	2.15	A	2-843	[»]
3T3G	X-ray	2.40	A	2-843	[»]
3T3H	X-ray	2.60	A	2-843	[»]
3T3I	X-ray	2.65	A	2-843	[»]
4EJ2	X-ray	2.65	A	13-837	[»]
4EKE	X-ray	2.60	A	13-837	[»]
4EKY	X-ray	2.45	A	13-837	[»]
4EL0	X-ray	2.40	A	13-837	[»]
4EL5	X-ray	2.00	A	13-837	[»]
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	[»]

ProteinModelPortal

P00489.

SMR

P00489. Positions 15-843.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-38240N.

IntAct

P00489. 1 interaction.

MINT

MINT-6368963.

Protein family/group databases

CAZy

GT35. Glycosyltransferase Family 35.

Proteomic databases

PRIDE

P00489.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

100008972.

Organism-specific databases

CTD

5837.

Phylogenomic databases

eggNOG

COG0058.

HOGENOM

HOG000278444.

HOVERGEN

HBG006848.

OrthoDB

EOG4S1T6F.

Enzyme and pathway databases

BRENDA

2.4.1.1. 1749.

SABIO-RK

P00489.

Family and domain databases

InterPro

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

PANTHER

PTHR11468. PTHR11468. 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

BindingDB

P00489.

ChEMBL

CHEMBL4696.

DrugBank

DB00131. Adenosine monophosphate.

EvolutionaryTrace

P00489.

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:	April 3, 2013
This is version 136 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families