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(-) Description

Title :  GLYCOCYAMINE KINASE, BETA-BETA HOMODIMER FROM MARINE WORM NAMALYCASTIS SP.
 
Authors :  K. Lim, S. Pullalarevu, O. Herzberg
Date :  15 Dec 09  (Deposition) - 02 Mar 10  (Release) - 11 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),D (1x)
Biol. Unit 4:  B,C  (1x)
Keywords :  Phosphagen Kinase, Glycocyamine Kinase, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Lim, S. Pullalarevu, K. T. Surabian, A. Howard, T. Suzuki, J. Moult, O. Herzberg
Structural Basis For The Mechanism And Substrate Specificit Of Glycocyamine Kinase, A Phosphagen Kinase Family Member.
Biochemistry V. 49 2031 2010
PubMed-ID: 20121101  |  Reference-DOI: 10.1021/BI9020988
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOCYAMINE KINASE BETA CHAIN
    Chains: A, B, C, D
    EC Number: 2.7.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGK_BETA221
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GK-BETA, GK_BETA
    Organism Scientific: NAMALYCASTIS SP. ST01
    Organism Taxid: 243920

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)  D (1x)
Biological Unit 4 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3L2D)

(-) Sites  (0, 0)

(no "Site" information available for 3L2D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L2D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:222 -Pro A:223
2Trp B:222 -Pro B:223
3Trp C:222 -Pro C:223
4Trp D:222 -Pro D:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L2D)

(-) Exons   (0, 0)

(no "Exon" information available for 3L2D)

(-) 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:367
 aligned with Q6AW42_9ANNE | Q6AW42 from UniProtKB/TrEMBL  Length:390

    Alignment length:367
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
         Q6AW42_9ANNE    24 KFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
               SCOP domains d3l2da1 A:24-113 automated matches                                                        d3l2da2 A:114-390 automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3l2dA01 A:24-113 Transferase Creatine Kinase, Chain A, domain 1                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhh............hhhhh.........eeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhh.eeeee....hhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee...........eeeeeeee..hhhhhhhhhhhhhhhheeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l2d A  24 KFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       


Chain B from PDB  Type:PROTEIN  Length:379
 aligned with Q6AW42_9ANNE | Q6AW42 from UniProtKB/TrEMBL  Length:390

    Alignment length:379
                                    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       301       311       321       331       341       351       361       371       381         
         Q6AW42_9ANNE    12 NRVGHSKPWESGKFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
               SCOP domains d3l2db1 B:12-113 automated matches                                                                    d3l2db2 B:114-390 automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3l2dB01 B:12-113 Transferase Creatine Kinase, Chain A, domain 1                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh............hhhhh.........eeeeeeeeee...........hhhhhhhhhhhhhhhhhh.hhhh.eeeee.hhhhhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee............eeeeeee........hhhhhhhhh.ee..............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l2d B  12 NRVGHSKPWESGKFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
                                    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       301       311       321       331       341       351       361       371       381         


Chain C from PDB  Type:PROTEIN  Length:367
 aligned with Q6AW42_9ANNE | Q6AW42 from UniProtKB/TrEMBL  Length:390

    Alignment length:367
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
         Q6AW42_9ANNE    24 KFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
               SCOP domains d3l2dc1 C:24-113 automated matches                                                        d3l2dc2 C:114-390 automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3l2dC01 C:24-113 Transferase Creatine Kinase, Chain A, domain 1                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh............hhhhh.........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh......ee...ee...........eeeeeeee..hhhhh.hhhhhhhhhheeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l2d C  24 KFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       


Chain D from PDB  Type:PROTEIN  Length:379
 aligned with Q6AW42_9ANNE | Q6AW42 from UniProtKB/TrEMBL  Length:390

    Alignment length:379
                                    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       301       311       321       331       341       351       361       371       381         
         Q6AW42_9ANNE    12 NRVGHSKPWESGKFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
               SCOP domains d3l2dd1 D:12-113 automated matches                                                                    d3l2dd2 D:114-390 automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3l2dD01 D:12-113 Transferase Creatine Kinase, Chain A, domain 1                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------ATP-gua_PtransN-3l2dD05 D:32-112                                                 ------------------ATP-gua_Ptrans-3l2dD01 D:131-378                                                                                                                                                                                                                        ------------ Pfam domains (1)
           Pfam domains (2) --------------------ATP-gua_PtransN-3l2dD06 D:32-112                                                 ------------------ATP-gua_Ptrans-3l2dD02 D:131-378                                                                                                                                                                                                                        ------------ Pfam domains (2)
           Pfam domains (3) --------------------ATP-gua_PtransN-3l2dD07 D:32-112                                                 ------------------ATP-gua_Ptrans-3l2dD03 D:131-378                                                                                                                                                                                                                        ------------ Pfam domains (3)
           Pfam domains (4) --------------------ATP-gua_PtransN-3l2dD08 D:32-112                                                 ------------------ATP-gua_Ptrans-3l2dD04 D:131-378                                                                                                                                                                                                                        ------------ Pfam domains (4)
         Sec.struct. author ......hhhhhh..hhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh............hhhhh.........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee............eeeeeee..hhhhh.hhhhhhhhhheeeee...........eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l2d D  12 NRVGHSKPWESGKFKAADNFPDLSKHNNVMASQLTKELYEKYWDKVTPNGVTFDKCIQTGVDNPGNKFYGKKTGCVFGDEYSYECYKEFFDKCIEEIHHFKPSDKHPAPDLDHNKLVGGVFEDKYVKSCRIRCGRSVKGVCLPPAMSRAERRLVEKVVSDALGGLKGDLAGKYYPLTTMNEKDQEQLIEDHFLFEKPTGALLTTSGCARDWPDGRGIWHNNEKNFLVWINEEDHIRVISMQKGGDLKAVFSRFARGLLEVERLMKECGHGLMHNDRLGYICTCPTNMGTVVRASVHLRLAFLEKHPRFDEMLGKLRLGKRGTGGESSLATDSTYDISNWARLGKSERELVQVLVDGVNLLIACDKKLEAGQSIDDMIPK 390
                                    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       301       311       321       331       341       351       361       371       381
   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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: GCS (23)
(-)
Clan: no clan defined [family: ATP-gua_PtransN] (14)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6AW42_9ANNE | Q6AW42)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q6AW42_9ANNE | Q6AW42: 3l2e 4v7n

(-) Related Entries Specified in the PDB File

3l2e 3l2f 3l2g