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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL C1 DOMAIN OF KAIC
 
Authors :  J. Abe, T. B. Hiyama, A. Mukaiyama, S. Son, S. Akiyama
Date :  29 May 14  (Deposition) - 01 Jul 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abe, T. B. Hiyama, A. Mukaiyama, S. Son, T. Mori, S. Saito, M. Osako, J. Wolanin, E. Yamashita, T. Kondo, S. Akiyama
Circadian Rhythms. Atomic-Scale Origins Of Slowness In The Cyanobacterial Circadian Clock.
Science V. 349 312 2015
PubMed-ID: 26113637  |  Reference-DOI: 10.1126/SCIENCE.1261040

(-) Compounds

Molecule 1 - CIRCADIAN CLOCK PROTEIN KINASE KAIC
    Chains: A, B, C, D, E, F
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-253
    Gene: KAIC, SYNPCC7942_1216, SEE0011
    Mutation: YES
    Organism Scientific: SYNECHOCOCCUS ELONGATUS PCC 7942
    Organism Taxid: 1140
    Strain: PCC 7942

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1AGS6Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2CL6Ligand/IonCHLORIDE ION
3MG6Ligand/IonMAGNESIUM ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:53 , AGS A:303 , HOH A:525 , HOH A:526 , HOH A:527binding site for residue MG A 301
02AC2SOFTWAREARG A:218 , ILE A:239binding site for residue CL A 302
03AC3SOFTWARETHR A:48 , GLY A:49 , THR A:50 , GLY A:51 , LYS A:52 , THR A:53 , LEU A:54 , SER A:89 , PHE A:90 , ARG A:218 , ILE A:239 , THR A:240 , ASP A:241 , MG A:301 , HOH A:413 , HOH A:462 , HOH A:504 , HOH A:525 , HOH A:526 , HOH A:527 , PHE B:199 , LYS B:224 , LEU B:225 , ARG B:226 , THR B:228 , HIS B:230 , HOH B:445binding site for residue AGS A 303
04AC4SOFTWARETHR B:53 , AGS B:303 , HOH B:552 , HOH B:553 , HOH B:554binding site for residue MG B 301
05AC5SOFTWAREARG B:218 , THR B:238 , ILE B:239 , HOH B:565binding site for residue CL B 302
06AC6SOFTWARETHR B:48 , GLY B:49 , THR B:50 , GLY B:51 , LYS B:52 , THR B:53 , LEU B:54 , SER B:89 , PHE B:90 , ARG B:218 , ILE B:239 , THR B:240 , ASP B:241 , MG B:301 , HOH B:422 , HOH B:552 , HOH B:553 , HOH B:554 , HOH B:555 , PHE C:199 , LYS C:224 , LEU C:225 , ARG C:226 , THR C:228 , HIS C:230 , HOH C:424binding site for residue AGS B 303
07AC7SOFTWARETHR C:53 , AGS C:303 , HOH C:553 , HOH C:554 , HOH C:555binding site for residue MG C 301
08AC8SOFTWAREARG C:218 , THR C:238 , ILE C:239binding site for residue CL C 302
09AC9SOFTWARETHR C:48 , GLY C:49 , THR C:50 , GLY C:51 , LYS C:52 , THR C:53 , LEU C:54 , SER C:89 , PHE C:90 , ARG C:218 , ILE C:239 , ASP C:241 , MG C:301 , HOH C:418 , HOH C:454 , HOH C:546 , HOH C:553 , HOH C:554 , HOH C:555 , HOH C:574 , PHE D:199 , LYS D:224 , LEU D:225 , ARG D:226 , THR D:228 , SER D:229 , HIS D:230 , HOH D:435binding site for residue AGS C 303
10AD1SOFTWARETHR D:53 , AGS D:303 , HOH D:543 , HOH D:544 , HOH D:545binding site for residue MG D 301
11AD2SOFTWAREARG D:218 , THR D:238 , ILE D:239 , HOH D:496binding site for residue CL D 302
12AD3SOFTWARETHR D:48 , GLY D:49 , THR D:50 , GLY D:51 , LYS D:52 , THR D:53 , LEU D:54 , SER D:89 , PHE D:90 , ARG D:218 , ILE D:239 , THR D:240 , ASP D:241 , MG D:301 , HOH D:434 , HOH D:453 , HOH D:543 , HOH D:544 , HOH D:545 , HOH D:567 , PHE E:199 , LYS E:224 , LEU E:225 , ARG E:226 , THR E:228 , SER E:229 , HIS E:230 , HOH E:432 , HOH E:489binding site for residue AGS D 303
13AD4SOFTWARETHR E:53 , AGS E:303 , HOH E:514 , HOH E:515 , HOH E:516binding site for residue MG E 301
14AD5SOFTWAREARG E:218 , THR E:238 , ILE E:239binding site for residue CL E 302
15AD6SOFTWARETHR E:48 , GLY E:49 , THR E:50 , GLY E:51 , LYS E:52 , THR E:53 , LEU E:54 , SER E:89 , PHE E:90 , ARG E:218 , ILE E:239 , THR E:240 , ASP E:241 , MG E:301 , HOH E:429 , HOH E:499 , HOH E:500 , HOH E:514 , HOH E:515 , HOH E:516 , PHE F:199 , LYS F:224 , LEU F:225 , ARG F:226 , THR F:228 , SER F:229 , HIS F:230 , HOH F:475binding site for residue AGS E 303
16AD7SOFTWARETHR F:53 , ASP F:145 , AGS F:303 , HOH F:509 , HOH F:510 , HOH F:511binding site for residue MG F 301
17AD8SOFTWAREARG F:218 , THR F:238 , ILE F:239 , HOH F:481binding site for residue CL F 302
18AD9SOFTWAREPHE A:199 , LYS A:224 , LEU A:225 , ARG A:226 , GLY A:227 , THR A:228 , SER A:229 , HIS A:230 , HOH A:423 , THR F:48 , GLY F:49 , THR F:50 , GLY F:51 , LYS F:52 , THR F:53 , LEU F:54 , SER F:89 , PHE F:90 , ARG F:218 , ILE F:239 , ASP F:241 , MG F:301 , HOH F:430 , HOH F:509 , HOH F:510 , HOH F:511binding site for residue AGS F 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TL9)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asp A:145 -Ser A:146
2Pro A:248 -Leu A:249
3Asp B:145 -Ser B:146
4Asp C:145 -Ser C:146
5Asp D:145 -Ser D:146
6Asp E:145 -Ser E:146
7Phe F:121 -Asp F:122
8Asp F:145 -Ser F:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TL9)

(-) Exons   (0, 0)

(no "Exon" information available for 4TL9)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl9 A  14 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTTGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 249
                                    23        33        43        53        63        73        83        93       103       121       131       141    || 159       169       179       189       199       209       219       229       239       249
                                                                                                                            112|                      146|                                                                                              
                                                                                                                             121                       155                                                                                              


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl9 B  16 QAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTTGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 249
                                    25        35        45        55        65        75        85        95       105      |123       133       143  ||   161       171       181       191       201       211       221       231       241        
                                                                                                                          112|                      146|                                                                                              
                                                                                                                           121                       155                                                                                              


Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee........hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tl9 C  14 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTTGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 249
                                    23        33        43        53        63        73        83        93       103       113|      129       139      |157       167       177       187       197       207       217       227       237       247  
                                                                                                                             113|                       146|                                                                                              
                                                                                                                              120                        155                                                                                              


Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl9 D  13 SEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTTGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLG 250
                                    22        32        42        52        62        72        82        92       102       122       132       142   ||  160       170       180       190       200       210       220       230       240       250
                                                                                                                           110|                      146|                                                                                               
                                                                                                                            121                       155                                                                                               


Chain E from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh.hhhhhhhh..eeeee......hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhhh.eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl9 E  16 QAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTTGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 249
                                    25        35        45        55        65        75        85        95       105      |123       133       143  ||   161       171       181       191       201       211       221       231       241        
                                                                                                                          112|                      146|                                                                                              
                                                                                                                           121                       155                                                                                              


Chain F from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....hhhhhh...ee...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh...hhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee............hhhhh..eeeeeeeeee..eeeeeeeeeee........eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tl9 F  18 IAKMRTMIEGFDDISHGGLPIGRSTLVSGTTGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDFDLSALIERINYAIQKYRARRVSIDSDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFP 248
                                    27        37        47        57        67        77        87        97       107   ||  126       136       146|      164       174       184       194       204       214       224       234       244    
                                                                                                                       111|                      146|                                                                                             
                                                                                                                        121                       155
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 4TL9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TL9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TL9)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:145 - Ser A:146   [ RasMol ]  
    Asp B:145 - Ser B:146   [ RasMol ]  
    Asp C:145 - Ser C:146   [ RasMol ]  
    Asp D:145 - Ser D:146   [ RasMol ]  
    Asp E:145 - Ser E:146   [ RasMol ]  
    Asp F:145 - Ser F:146   [ RasMol ]  
    Phe F:121 - Asp F:122   [ RasMol ]  
    Pro A:248 - Leu A:249   [ RasMol ]  
 

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  4tl9
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  KAIC_SYNE7 | Q79PF4
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        KAIC_SYNE7 | Q79PF4: 1tf7 1u9i 2gbl 3dvl 3jzm 3k09 3k0a 3k0c 3k0e 3k0f 3s1a 4dug 4ijm 4tl6 4tl7 4tl8 4tla 4tlb 4tlc 4tld 4tle 5c5e 5n8y

(-) Related Entries Specified in the PDB File

4tl6 4tl7 4tl8 4tla 4tlb 4tlc 4tld 4tle