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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHIMERICAL MUTANT CAPABK55M PROTEIN
 
Authors :  V. Olivares-Illana, P. Meyer, V. Gueguen-Chaignon, D. Soulat, J. Deustcher, A. J. Cozzone, S. Morera, C. Grangeasse, S. Nessler
Date :  19 Oct 07  (Deposition) - 01 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Co-Polymerase, Activation Mechanism, Chimera, Transferase, Bacterial Tyrosine-Kinase, Exopolysaccharide Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Olivares-Illana, P. Meyer, E. Bechet, V. Gueguen-Chaignon, D. Soulat, S. Lazereg-Riquier, I. Mijakovic, J. Deutscher, A. J. Cozzone, O. Laprevote, S. Morera, C. Grangeasse, S. Nessler
Structural Basis For The Regulation Mechanism Of The Tyrosine Kinase Capb From Staphylococcus Aureus.
Plos Biol. V. 6 E143 2008
PubMed-ID: 18547145  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0060143

(-) Compounds

Molecule 1 - MEMBRANE PROTEIN CAPA1, PROTEIN TYROSINE KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: THE LAST 29AA FROM CAPA1, RESIDUES 197-222,
    Gene: CAPA1, CAPB2
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: BOUND ADP AND MG
    Synonym: CHIMERICAL PROTEIN CAPAB, CAP5A

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1ADP8Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:219 , LYS A:220 , PHE A:221 , SER A:1010 , GLY A:1052 , ALA A:1053 , GLY A:1054 , MET A:1055 , SER A:1056 , THR A:1057 , ASN A:1211 , ARG A:1212 , HOH A:2056 , HOH A:2057 , MG A:2228 , ASN B:1103 , TRP B:1104 , SER B:1105 , THR B:1106BINDING SITE FOR RESIDUE ADP A2227
2AC2SOFTWAREGLN B:219 , LYS B:220 , PHE B:221 , SER B:1010 , GLY B:1052 , ALA B:1053 , GLY B:1054 , MET B:1055 , SER B:1056 , THR B:1057 , ASN B:1211 , ARG B:1212 , HOH B:2055 , MG B:2230BINDING SITE FOR RESIDUE ADP B2229
3AC3SOFTWARESER A:1056 , ADP A:2227BINDING SITE FOR RESIDUE MG A2228
4AC4SOFTWARESER B:1056 , ASP B:1157 , THR B:1158 , ADP B:2229BINDING SITE FOR RESIDUE MG B2230

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VED)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:1225 -Gly A:1226
2Asp B:1216 -Lys B:1217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VED)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VED)

(-) Exons   (0, 0)

(no "Exon" information available for 2VED)

(-) 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:252
 aligned with A8YPQ5_STAAU | A8YPQ5 from UniProtKB/TrEMBL  Length:230

    Alignment length:252
                                                      1                                                                                                                                                                                                                                 
                                     -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224  
        A8YPQ5_STAAU      - --------------------------MTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPKDKSASYYAYYG  226
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeee.............hhhhhh..hhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh......hhhhhhh...hhhhheee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh...eeeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ved A  197 DKRIKDEEDVEKELGLPVLGSIQKFNMTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGMSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPKDKSASYYAYYG 1226
                                   206       216     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224  
                                                   222|                                                                                                                                                                                                                                 
                                                   1001                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with A8YPQ5_STAAU | A8YPQ5 from UniProtKB/TrEMBL  Length:230

    Alignment length:254
                                                      1                                                                                                                                                                                                                                   
                                     -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
        A8YPQ5_STAAU      - --------------------------MTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGKSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPKDKSASYYAYYGTD  228
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------AAA_31-2vedB01 B:1042-1190                                                                                                                           -------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------AAA_31-2vedB02 B:1042-1190                                                                                                                           -------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhh..eeeeee.............hhhhhh..hhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh......hhhhhhh...hhhhhhee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh...eeeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ved B  197 DKRIKDEEDVEKELGLPVLGSIQKFNMTNTRRSTSSLIVHEQPKSPISEKFRGIRSNIMFANPDSAVQSIVITSEAPGAGMSTIAANLAVAYAQAGYKTLIVDGDMRKPTQHYIFNLPNNEGLSSLLLNWSTYQDSIISTEIEDLDVLTSGPIPPNPSELITSRAFANLYDTLLMNYNFVIIDTPPVNTVTDAQLFSKFTGNVVYVVNSENNNKDEVKKGKELIEATGAKLLGVVLNRMPKDKSASYYAYYGTD 1228
                                   206       216     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224    
                                                   222|                                                                                                                                                                                                                                   
                                                   1001
   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  (0, 0)

(no "SCOP Domain" information available for 2VED)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VED)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: AAA_31 (4)
(-)
Staphylococcus aureus (1)
1aAAA_31-2vedB01B:1042-1190
1bAAA_31-2vedB02B:1042-1190

(-) Gene Ontology  (14, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A8YPQ5_STAAU | A8YPQ5)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    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.
biological process
    GO:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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
        A8YPQ5_STAAU | A8YPQ5: 3bfv 4jmp
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