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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE FROM LISTARIA MONOCYTIGENES
 
Authors :  M. M. Klimecka, M. Chruszcz, M. D. Zimmerman, M. Kudritska, A. Savchenk A. Edwards, A. Joachimiak, W. Minor, Midwest Center For Structura Genomics (Mcsg)
Date :  08 Dec 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Eal-Domain, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Klimecka, M. Chruszcz, M. D. Zimmerman, M. Kudritska, A. Savchenko, A. Edwards, A. Joachimiak, W. Minor
Crystal Structure Of Putative Diguanylate Cyclase/Phosphodiesterase From Listaria Monocytigenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LMO0111
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Synonym: LMO0111 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CAC2Ligand/IonCACODYLATE ION
3CL6Ligand/IonCHLORIDE ION
4MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:222 , ILE A:223 , HOH A:294 , HOH A:343BINDING SITE FOR RESIDUE CL A 236
02AC2SOFTWARELEU A:28 , ASN A:78 , HOH A:280 , HOH A:382BINDING SITE FOR RESIDUE CL A 237
03AC3SOFTWARESER A:150 , SER B:150BINDING SITE FOR RESIDUE CL A 238
04AC4SOFTWAREPHE A:176 , ASN A:178 , ILE A:179 , HOH A:371 , MSE B:160BINDING SITE FOR RESIDUE CL A 239
05AC5SOFTWAREGLU A:25 , ASN A:78 , GLU A:106 , ASP A:147 , HOH A:303 , HOH A:472BINDING SITE FOR RESIDUE CA A 240
06AC6SOFTWAREARG A:74 , HOH A:320 , HOH A:470 , HOH A:507BINDING SITE FOR RESIDUE CAC A 241
07AC7SOFTWARELEU B:28 , ASN B:78 , HOH B:271BINDING SITE FOR RESIDUE CL B 236
08AC8SOFTWAREGLU B:25 , ASN B:78 , GLU B:106 , ASP B:147 , HOH B:300 , HOH B:338BINDING SITE FOR RESIDUE CA B 237
09AC9SOFTWAREPHE B:85 , TYR B:86 , ILE B:87 , HIS B:117BINDING SITE FOR RESIDUE CL B 238
10BC1SOFTWAREARG B:74 , HOH B:267BINDING SITE FOR RESIDUE CAC B 239

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KZP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KZP)

(-) 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:231
 aligned with Q8YAK7_LISMO | Q8YAK7 from UniProtKB/TrEMBL  Length:235

    Alignment length:231
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
         Q8YAK7_LISMO     5 KFQLFIQPKLDVLQGNIVEYEILLRDDSAVPRFPLSELEAVLADEELYLAFSEWFSEAFLDVLKKYPNDRFAINIAPQQLFYIETLHWLDKLKSESHRITVEMTEDIFDVPGHKRHLNANDKNAFILNKIKVIHGLGYHIAIDDVSCGLNSLERVMSYLPYIIEIKFSLIHFKNIPLEDLLLFIKAWANFAQKNKLDFVVEGIETKETMTLLESHGVSIFQGYLVNKPFPV 235
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhh..hhhhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.....eeee....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzp A   5 KFQLFIQPKLDVLQGNIVEYEILLRDDSAVPRFPLSELEAVLADEELYLAFSEWFSEAFLDVLKKYPNDRFAINIAPQQLFYIETLHWLDKLKSESHRITVEmTEDIFDVPGHKRHLNANDKNAFILNKIKVIHGLGYHIAIDDVSCGLNSLERVmSYLPYIIEIKFSLIHFKNIPLEDLLLFIKAWANFAQKNKLDFVVEGIETKETmTLLESHGVSIFQGYLVNKPFPV 235
                                    14        24        34        44        54        64        74        84        94       104  |    114       124       134       144       154     | 164       174       184       194       204       214       224       234 
                                                                                                                                107-MSE                                              160-MSE                                              213-MSE                  


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with Q8YAK7_LISMO | Q8YAK7 from UniProtKB/TrEMBL  Length:235

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
         Q8YAK7_LISMO     4 MKFQLFIQPKLDVLQGNIVEYEILLRDDSAVPRFPLSELEAVLADEELYLAFSEWFSEAFLDVLKKYPNDRFAINIAPQQLFYIETLHWLDKLKSESHRITVEMTEDIFDVPGHKRHLNANDKNAFILNKIKVIHGLGYHIAIDDVSCGLNSLERVMSYLPYIIEIKFSLIHFKNIPLEDLLLFIKAWANFAQKNKLDFVVEGIETKETMTLLESHGVSIFQGYLVNKPFPV 235
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) EAL-3kzpB01 B:4-232                                                                                                                                                                                                                  --- Pfam domains (1)
           Pfam domains (2) EAL-3kzpB02 B:4-232                                                                                                                                                                                                                  --- Pfam domains (2)
         Sec.struct. author ...eeeeeeee......eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh.eeeee.......hhhhh..hhhhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh.....eeee....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzp B   4 mKFQLFIQPKLDVLQGNIVEYEILLRDDSAVPRFPLSELEAVLADEELYLAFSEWFSEAFLDVLKKYPNDRFAINIAPQQLFYIETLHWLDKLKSESHRITVEmTEDIFDVPGHKRHLNANDKNAFILNKIKVIHGLGYHIAIDDVSCGLNSLERVmSYLPYIIEIKFSLIHFKNIPLEDLLLFIKAWANFAQKNKLDFVVEGIETKETmTLLESHGVSIFQGYLVNKPFPV 235
                            |       13        23        33        43        53        63        73        83        93       103   |   113       123       133       143       153      |163       173       183       193       203       213       223       233  
                            4-MSE                                                                                                107-MSE                                              160-MSE                                              213-MSE
   Legend:   → Mismatch (orange background)
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  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 3KZP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KZP)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: EAL] (10)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8YAK7_LISMO | Q8YAK7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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