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(-) Description

Title :  THE CATALYTIC MECHANISM OF PHOSPHORYLASE KINASE PROBED BY MUTATIONAL STUDIES
 
Authors :  V. T. Skamnaki, D. J. Owen, M. E. M. Noble, E. D. Lowe, N. G. Oikonomakos, L. N. Johnson
Date :  24 Aug 99  (Deposition) - 14 Dec 99  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase (Glycogen Metabolism), Glycogen Metabolism, Transferase, Serine/Threonine-Protein, Kinase, Atp-Binding, Calmodulin-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. T. Skamnaki, D. J. Owen, M. E. Noble, E. D. Lowe, G. Lowe, N. G. Oikonomakos, L. N. Johnson
Catalytic Mechanism Of Phosphorylase Kinase Probed By Mutational Studies.
Biochemistry V. 38 14718 1999
PubMed-ID: 10545198  |  Reference-DOI: 10.1021/BI991454F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORYLASE KINASE
    Chains: A
    EC Number: 2.7.1.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMW172
    Expression System Taxid: 562
    Fragment: GAMMA SUBUNIT, TRUNCATED TO RESIDUES 1 - 298
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Other Details: LIGANDS ATP AND MN(II)
    Synonym: RABBIT MUSCLE PHOSPHORYLASE KINASE
    Tissue: SKELETAL MUSCLE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:167 , ATP A:301 , HOH A:467BINDING SITE FOR RESIDUE MN B 382
2AC2SOFTWAREASN A:154 , ASP A:167 , ATP A:301 , HOH A:402BINDING SITE FOR RESIDUE MN B 383
3AC3SOFTWARELYS A:72 , ARG A:148 , LEU A:180 , HOH A:448 , HOH A:415BINDING SITE FOR RESIDUE SO4 C 401
4AC4SOFTWARELEU A:25 , GLY A:26 , GLY A:28 , SER A:31 , VAL A:33 , ALA A:46 , LYS A:48 , ASP A:104 , MET A:106 , GLU A:110 , LYS A:124 , GLU A:153 , ASN A:154 , LEU A:156 , ASP A:167 , MN A:302 , MN A:303 , HOH A:447 , HOH A:422 , HOH A:402BINDING SITE FOR RESIDUE ATP B 381

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QL6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QL6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QL6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PHKG1_RABIT26-49  1A:25-48
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PHKG1_RABIT146-158  1A:145-157

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSOCUT000000136151ENSOCUE00000243534Un0090:781787-78184761PHKG1_RABIT-00--
1.2ENSOCUT000000136152ENSOCUE00000222370Un0090:784235-784336102PHKG1_RABIT1-28281A:11-2717
1.3ENSOCUT000000136153ENSOCUE00000159051Un0090:785464-785648185PHKG1_RABIT28-90631A:27-8963
1.4ENSOCUT000000136154ENSOCUE00000292633Un0090:785983-78603755PHKG1_RABIT90-108191A:89-10719
1.5ENSOCUT000000136155ENSOCUE00000159073Un0090:787798-78786366PHKG1_RABIT108-130231A:107-12923
1.6ENSOCUT000000136156ENSOCUE00000159085Un0090:787992-788155164PHKG1_RABIT130-185561A:129-18456
1.7ENSOCUT000000136157ENSOCUE00000247647Un0090:788562-78865291PHKG1_RABIT185-215311A:184-21431
1.8ENSOCUT000000136158ENSOCUE00000159109Un0090:788761-788914154PHKG1_RABIT215-266521A:214-26552
1.9ENSOCUT000000136159ENSOCUE00000159120Un0090:789079-789204126PHKG1_RABIT267-308421A:266-29126
1.10ENSOCUT0000001361510ENSOCUE00000159128Un0090:789525-790385861PHKG1_RABIT309-389810--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:281
 aligned with PHKG1_RABIT | P00518 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:281
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
          PHKG1_RABIT    12 STHGFYENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSGHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVTLSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGEKLREVCGTPSYLAPEIIECSMNDNHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSPEWDDYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQYV 292
               SCOP domains d1ql6a_ A: gamma-subunit of glycogen phosphorylase kinase (Phk)                                                                                                                                                                                                                           SCOP domains
               CATH domains ----1ql6A01 A:15-105 Phosphorylase Kinase; domain 1                                            1ql6A02 A:106-291 Transferase(Phosphotransferase) domain 1                                                                                                                                 CATH domains
               Pfam domains --------Pkinase-1ql6A01 A:19-287                                                                                                                                                                                                                                                     ---- Pfam domains
         Sec.struct. author hhhhhhhheee..eeee...eeeeeeee....eeeeeeeee........hhhhhhhhhhhhhhhhhhhhh........eeeeee...eeeeeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhheee.....eee.....................hhh..hhhhhhhh........hhhhhhhhhhhhhhhhh.........hhhhhhhhhh.........hhh..hhhhhhhhhh....hhh...hhhhhh.hhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2         -------------------------------------------------------------Exon 1.4           ---------------------Exon 1.6  PDB: A:129-184 UniProt: 130-185               -----------------------------Exon 1.8  PDB: A:214-265 UniProt: 215-266           Exon 1.9  PDB: A:266-291   Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.3  PDB: A:27-89 UniProt: 28-90                          -----------------Exon 1.5  PDB: A:107-12------------------------------------------------------Exon 1.7  PDB: A:184-214       ----------------------------------------------------------------------------- Transcript 1 (2)
                 1ql6 A  11 STHGFYENYEPKEILGRGVSSVVRRCIHKPTCKEYAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSGHPNIIQLKDTYETNTFFFLVFDLMKKGELFDYLTEKVTLSEKETRKIMRALLEVICALHKLNIVHRDLKPENILLDDDMNIKLTDFGFSCQLDPGEKLRSVCGTPSYLAPEIIECSMNDNHPGYGKEVDMWSTGVIMYTLLAGSPPFWHRKQMLMLRMIMSGNYQFGSPEWDDYSDTVKDLVSRFLVVQPQKRYTAEEALAHPFFQQYV 291
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHKG1_RABIT | P00518)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004689    phosphorylase kinase activity    Catalysis of the reaction: 4 ATP + 2 phosphorylase b = 4 ADP + phosphorylase a.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0050321    tau-protein kinase activity    Catalysis of the reaction: ATP + tau-protein = ADP + O-phospho-tau-protein.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0005978    glycogen biosynthetic process    The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
    GO:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005964    phosphorylase kinase complex    An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PHKG1_RABIT | P00518: 1phk 2phk

(-) Related Entries Specified in the PDB File

1phk TWO STRUCTURES OF THE CATALYTIC DOMAIN OF PHOSPHORYLASE, KINASE: AN ACTIVE PROTEIN KINASE COMPLEXED WITH NUCLEOTIDE, SUBSTRATE-ANALOGUE AND PRODUCT
2phk THE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE COMPLEX: KINASE SUBSTRATE RECOGNITION