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(-) Description

Title :  CRYSTAL STRUCTURE OF CAMP-FREE R1A SUBUNIT OF PKA
 
Authors :  J. Wu, S. Brown, N. -H. Xuong, S. S. Taylor
Date :  24 Nov 03  (Deposition) - 06 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Type 1A Regulatory Subunit, Camp-Dependent Protein Kinase, Camp-Free, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Wu, S. Brown, N. H. Xuong, S. S. Taylor
Rialpha Subunit Of Pka: A Camp-Free Structure Reveals A Hydrophobic Capping Mechanism For Docking Camp Into Site B.
Structure V. 12 1057 2004
PubMed-ID: 15274925  |  Reference-DOI: 10.1016/J.STR.2004.03.022

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE TYPE I-ALPHA REGULATORY CHAIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePRKAR1A
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2PCG2Ligand/IonCYCLIC GUANOSINE MONOPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PCG1Ligand/IonCYCLIC GUANOSINE MONOPHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PCG1Ligand/IonCYCLIC GUANOSINE MONOPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:182 , PHE A:198 , GLY A:199 , GLU A:200 , LEU A:201 , ALA A:202 , ARG A:209 , ALA A:210 , TRP A:260BINDING SITE FOR RESIDUE PCG A 401
2AC2SOFTWAREPHE A:374 , PHE B:598 , GLY B:599 , GLU B:600 , LEU B:601 , ALA B:602 , PRO B:608 , ARG B:609 , ALA B:610 , ALA B:611 , TRP B:660BINDING SITE FOR RESIDUE PCG B 801
3AC3SOFTWAREGLY A:323 , ILE A:325 , ALA A:326BINDING SITE FOR RESIDUE GOL A 402
4AC4SOFTWAREGLY B:723 , ILE B:725 , ALA B:726 , ALA B:734 , ALA B:735BINDING SITE FOR RESIDUE GOL B 802
5AC5SOFTWAREGLY B:559 , GLU B:560 , THR B:561 , LYS B:614BINDING SITE FOR RESIDUE GOL B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RL3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RL3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RL3)

(-) PROSITE Motifs  (3, 12)

Asymmetric Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.KAP0_BOVIN136-251
 
254-375
 
  4A:135-250
B:535-650
A:253-374
B:653-767
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.KAP0_BOVIN163-179
 
281-297
 
  4A:162-178
B:562-578
A:280-296
B:680-696
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.KAP0_BOVIN199-216
 
323-340
 
  4A:198-215
B:598-615
A:322-339
B:722-739
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.KAP0_BOVIN136-251
 
254-375
 
  2A:135-250
-
A:253-374
-
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.KAP0_BOVIN163-179
 
281-297
 
  2A:162-178
-
A:280-296
-
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.KAP0_BOVIN199-216
 
323-340
 
  2A:198-215
-
A:322-339
-
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.KAP0_BOVIN136-251
 
254-375
 
  2-
B:535-650
-
B:653-767
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.KAP0_BOVIN163-179
 
281-297
 
  2-
B:562-578
-
B:680-696
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.KAP0_BOVIN199-216
 
323-340
 
  2-
B:598-615
-
B:722-739

(-) Exons   (9, 18)

Asymmetric Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000113711ENSBTAE00000313083chr19:63667746-63667642105KAP0_BOVIN-00--
1.2ENSBTAT000000113712ENSBTAE00000092376chr19:63665339-63665143197KAP0_BOVIN1-59590--
1.3ENSBTAT000000113713ENSBTAE00000092377chr19:63660511-63660341171KAP0_BOVIN60-116572A:109-115
B:509-515
7
7
1.4ENSBTAT000000113714ENSBTAE00000092378chr19:63659532-6365944192KAP0_BOVIN117-147312A:116-146
B:516-546
31
31
1.5ENSBTAT000000113715ENSBTAE00000092380chr19:63659241-6365918062KAP0_BOVIN147-168222A:146-167
B:546-567
22
22
1.6ENSBTAT000000113716ENSBTAE00000092381chr19:63658431-6365838547KAP0_BOVIN168-183162A:167-182
B:567-582
16
16
1.7ENSBTAT000000113717ENSBTAE00000092382chr19:63657530-63657372159KAP0_BOVIN184-236532A:183-235
B:583-635
53
53
1.8ENSBTAT000000113718ENSBTAE00000092383chr19:63656713-6365665361KAP0_BOVIN237-257212A:236-256
B:636-656
21
21
1.9ENSBTAT000000113719ENSBTAE00000092384chr19:63655618-63655497122KAP0_BOVIN257-297412A:256-296
B:656-696
41
41
1.10ENSBTAT0000001137110ENSBTAE00000092385chr19:63654637-6365455682KAP0_BOVIN298-325282A:297-324
B:697-724
28
28
1.11ENSBTAT0000001137111ENSBTAE00000092386chr19:63654278-63653922357KAP0_BOVIN325-381572A:324-376
B:724-767
53
44

(-) Sequences/Alignments

Asymmetric 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:268
 aligned with KAP0_BOVIN | P00514 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:268
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369        
           KAP0_BOVIN   110 ASYVRKVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKLDRPRFERVLGPCSDILKRNIQQYNSFVS 377
               SCOP domains d1rl3a1 A:109-244 Regulatory subunit of Protein kinase A                                                                                d1rl3a2 A:245-376 Regulatory subunit of Protein kinase A                                                                             SCOP domains
               CATH domains ----1rl3A01 A:113-234 Jelly Rolls                                                                                             1rl3A02 A:235-376 Jelly Rolls                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh......hhhhhhhhhhhheeeee....eeeee.....eeeeeee..eeeee..ee........eehhhhhhhh...eeeeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.................eeeeeee..eeeee............ee....eehhhhhhh.....eee......eeeeeehhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------CNMP_BINDING_3  PDB: A:135-250 UniProt: 136-251                                                                     --CNMP_BINDING_3  PDB: A:253-374 UniProt: 254-375                                                                           -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------CNMP_BINDING_1   -------------------CNMP_BINDING_2    ----------------------------------------------------------------CNMP_BINDING_1   -------------------------CNMP_BINDING_2    ------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.3    Exon 1.4  PDB: A:116-146       --------------------Exon 1.6        Exon 1.7  PDB: A:183-235 UniProt: 184-236            Exon 1.8             ----------------------------------------Exon 1.10  PDB: A:297-324   ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.5              ----------------------------------------------------------------------------------------Exon 1.9  PDB: A:256-296 UniProt: 257-297---------------------------Exon 1.11  PDB: A:324-376 UniProt: 325-381            Transcript 1 (2)
                 1rl3 A 109 ASYVRKVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKLDRPRFERVLGPCSDILKRNIQQYNSFVS 376
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368        

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with KAP0_BOVIN | P00514 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:259
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359         
           KAP0_BOVIN   110 ASYVRKVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKLDRPRFERVLGPCSDILKRN 368
               SCOP domains d1rl3b1 B:509-644 Regulatory subunit of Protein kinase A                                                                                d1rl3b2 B:645-767 Regulatory subunit of Protein kinase A                                                                    SCOP domains
               CATH domains ----1rl3B01 B:513-634 Jelly Rolls                                                                                             1rl3B02 B:635-767 Jelly Rolls                                                                                                         CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------cNMP_binding-1rl3B01 B:671-762                                                              ----- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------cNMP_binding-1rl3B02 B:671-762                                                              ----- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------cNMP_binding-1rl3B03 B:671-762                                                              ----- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------cNMP_binding-1rl3B04 B:671-762                                                              ----- Pfam domains (4)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh....hhhhhhhhhheeeee....eee.......eeeeeee..eeee.............eehhhhhhhh.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeeee..............eeeeeee..eeeee........eeeeee....ee..hhhhhh.....eee....eeeeeeehhhhhhhh..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------CNMP_BINDING_3  PDB: B:535-650 UniProt: 136-251                                                                     --CNMP_BINDING_3  PDB: B:653-767 UniProt: 254-375                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------------CNMP_BINDING_1   -------------------CNMP_BINDING_2    ----------------------------------------------------------------CNMP_BINDING_1   -------------------------CNMP_BINDING_2    ---------------------------- PROSITE (2)
           Transcript 1 (1) 1.3    Exon 1.4  PDB: B:516-546       --------------------Exon 1.6        Exon 1.7  PDB: B:583-635 UniProt: 184-236            Exon 1.8             ----------------------------------------Exon 1.10  PDB: B:697-724   ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.5              ----------------------------------------------------------------------------------------Exon 1.9  PDB: B:656-696 UniProt: 257-297---------------------------Exon 1.11  PDB: B:724-767 UniProt: 325-381   Transcript 1 (2)
                 1rl3 B 509 ASYVRKVIPKDYKTMAALAKAIEKNVLFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMDVYVNNEWATSVGEGGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKLDRPRFERVLGPCSDILKRN 767
                                   518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1rl3A01A:113-234
1b1rl3B01B:513-634
1c1rl3A02A:235-376
1d1rl3B02B:635-767

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KAP0_BOVIN | P00514)
molecular function
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0004862    cAMP-dependent protein kinase inhibitor activity    Stops, prevents or reduces the activity of a cAMP-dependent protein kinase.
    GO:0008603    cAMP-dependent protein kinase regulator activity    Modulation of the activity of the enzyme cAMP-dependent protein kinase.
    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:0034236    protein kinase A catalytic subunit binding    Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0060038    cardiac muscle cell proliferation    The expansion of a cardiac muscle cell population by cell division.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001707    mesoderm formation    The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:0046007    negative regulation of activated T cell proliferation    Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation.
    GO:2000480    negative regulation of cAMP-dependent protein kinase activity    Any process that stops, prevents or reduces the frequency, rate or extent of cAMP-dependent protein kinase activity.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0045214    sarcomere organization    The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
cellular component
    GO:0005952    cAMP-dependent protein kinase complex    An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031594    neuromuscular junction    The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
    GO:0031588    nucleotide-activated protein kinase complex    A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae).
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0044853    plasma membrane raft    A membrane raft that is part of the plasma membrane.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAP0_BOVIN | P005141apk 1bpk 1ne4 1ne6 1pvk 1rgs 2ezw 2qcs 3fhi 3iia 3im3 3im4 3plq 3pna 3pvb 4jv4 4mx3 4x6r 5hvz 5jr7

(-) Related Entries Specified in the PDB File

1ne4 CRYSTAL STRUCTURE OF RP-CAMP ANALOG BOUND R1A SUBUNIT OF PKA
1ne6 CRYSTAL STRUCTURE OF SP-CAMP ANALOG BOUND R1A SUBUNIT OF PKA
1rgs CRYSTAL STRUCTURE OF CAMP-BOUND R1A SUBUNIT OF PKA