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(-) Description

Title :  EAL DOMAIN OF PHOSPHODIESTERASE PDEA IN COMPLEX WITH 5'-PGPG AND MG++
 
Authors :  E. V. Filippova, G. Minasov, L. Shuvalova, O. Kiryukhina, C. Massa, T. S A. Joachimiak, W. F. Anderson, Midwest Center For Structural Gen (Mcsg)
Date :  03 Oct 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Ggdef, Eal, C-Digmp, Lyase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Filippova, G. Minasov, L. Shuvalova, O. Kiryukhina, C. Massa, T. Schirmer, A. Joachimiak, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Eal Domain From Caulobacter Crescentus In Complex With 5'-Pgpg And Mg++
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GGDEF FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 (DE3) MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CC_3396
    Organism Scientific: CAULOBACTER VIBRIOIDES
    Organism Taxid: 190650
    Strain: CB15
 
Molecule 2 - RNA (5'-R(P*GP*G)-3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1MG6Ligand/IonMAGNESIUM ION
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:323 , ASN A:384 , GLU A:416 , ASP A:446 , G C:601BINDING SITE FOR RESIDUE MG A 2
2AC2SOFTWAREASP A:446 , ASP A:447 , GLU A:503 , G C:601BINDING SITE FOR RESIDUE MG A 3
3AC3SOFTWAREHOH B:2 , GLU B:323 , ASN B:384 , GLU B:416 , ASP B:446 , G D:601BINDING SITE FOR RESIDUE MG B 1
4AC4SOFTWAREHOH B:80 , ASP B:446 , ASP B:447 , GLU B:503 , G D:601BINDING SITE FOR RESIDUE MG B 4
5AC5SOFTWAREHOH A:149 , HOH A:150 , HOH A:151 , G C:601 , G C:602BINDING SITE FOR RESIDUE MG C 5
6AC6SOFTWAREHOH B:65 , HOH D:64 , G D:601 , G D:602BINDING SITE FOR RESIDUE MG D 6

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U2E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U2E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U2E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U2E)

(-) Exons   (0, 0)

(no "Exon" information available for 3U2E)

(-) 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:260
 aligned with Q9A310_CAUCR | Q9A310 from UniProtKB/TrEMBL  Length:555

    Alignment length:260
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546
         Q9A310_CAUCR   287 SRLALEADLRGAIGRGEITPYFQPIVRLSTGALSGFEALARWIHPRRGMLPPDEFLPLIEEMGLMSELGAHMMHAAAQQLSTWRAAHPAMGNLTVSVNLSTGEIDRPGLVADVAETLRVNRLPRGALKLEVTESDIMRDPERAAVILKTLRDAGAGLALDDFGTGFSSLSYLTRLPFDTLKIDRYFVRTMGNNAGSAKIVRSVVKLGQDLDLEVVAEGVENAEMAHALQSLGCDYGQGFGYAPALSPQEAEVYLNEAYVD 546
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.......eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhh.hhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeehhhhhhhh..hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh....ee.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u2e A 287 SRLALEADLRGAIGRGEITPYFQPIVRLSTGALSGFEALARWIHPRRGmLPPDEFLPLIEEmGLmSELGAHmmHAAAQQLSTWRAAHPAmGNLTVSVNLSTGEIDRPGLVADVAETLRVNRLPRGALKLEVTESDImRDPERAAVILKTLRDAGAGLALDDFGTGFSSLSYLTRLPFDTLKIDRYFVRTmGNNAGSAKIVRSVVKLGQDLDLEVVAEGVENAEmAHALQSLGCDYGQGFGYAPALSPQEAEVYLNEAYVD 546
                                   296       306       316       326       336       346 |  |  356 ||    366       376       386       396       406       416      |426       436       446       456       466       476       486       496       506   |   516       526       536       546
                                                                          335-MSE      348-MSE     ||              376-MSE                                        423-MSE                                              476-MSE                           510-MSE                                
                                                                                          351-MSE  ||                                                                                                                                                                                           
                                                                                                 358-MSE                                                                                                                                                                                        
                                                                                                  359-MSE                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with Q9A310_CAUCR | Q9A310 from UniProtKB/TrEMBL  Length:555

    Alignment length:255
                                   295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535     
         Q9A310_CAUCR   286 LSRLALEADLRGAIGRGEITPYFQPIVRLSTGALSGFEALARWIHPRRGMLPPDEFLPLIEEMGLMSELGAHMMHAAAQQLSTWRAAHPAMGNLTVSVNLSTGEIDRPGLVADVAETLRVNRLPRGALKLEVTESDIMRDPERAAVILKTLRDAGAGLALDDFGTGFSSLSYLTRLPFDTLKIDRYFVRTMGNNAGSAKIVRSVVKLGQDLDLEVVAEGVENAEMAHALQSLGCDYGQGFGYAPALSPQEAEVYL 540
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhh.hhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhh.....eeeehhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh...eee........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u2e B 286 LSRLALEADLRGAIGRGEITPYFQPIVRLSTGALSGFEALARWIHPRRGmLPPDEFLPLIEEmGLmSELGAHmmHAAAQQLSTWRAAHPAmGNLTVSVNLSTGEIDRPGLVADVAETLRVNRLPRGALKLEVTESDImRDPERAAVILKTLRDAGAGLALDDFGTGFSSLSYLTRLPFDTLKIDRYFVRTmGNNAGSAKIVRSVVKLGQDLDLEVVAEGVENAEmAHALQSLGCDYGQGFGYAPALSPQEAEVYL 540
                                   295       305       315       325       335       345  |  | 355  ||   365       375|      385       395       405       415       425       435       445       455       465       475|      485       495       505    |  515       525       535     
                                                                           335-MSE      348-MSE     ||              376-MSE                                        423-MSE                                              476-MSE                           510-MSE                          
                                                                                           351-MSE  ||                                                                                                                                                                                     
                                                                                                  358-MSE                                                                                                                                                                                  
                                                                                                   359-MSE                                                                                                                                                                                 


Chain C from PDB  Type:RNA  Length:2
                                  
                 3u2e C 601 GG 602


Chain D from PDB  Type:RNA  Length:2
                                  
                 3u2e D 601 GG 602
   Legend:   → Mismatch (orange background)
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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 3U2E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U2E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U2E)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9A310_CAUCR | Q9A310)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9A310_CAUCR | Q9A310: 3u2a
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        Q9A310_CAUCR | Q9A310: 3s83 4hjf

(-) Related Entries Specified in the PDB File

3s83 RELATED ID: APC106607 RELATED DB: TARGETDB