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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE COMPLEX WITH CYCLIC DI-GMP
 
Authors :  C. Chang, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak, Midwes For Structural Genomics (Mcsg)
Date :  20 May 10  (Deposition) - 16 Jun 10  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ggdef & Eal Domains, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Tchigvintsev, X. Xu, A. Singer, C. Chang, G. Brown, M. Proudfoot, H. Cui, R. Flick, W. F. Anderson, A. Joachimiak, M. Y. Galperin, A. Savchenko, A. F. Yakunin
Structural Insight Into The Mechanism Of C-Di-Gmp Hydrolysi By Eal Domain Phosphodiesterases.
J. Mol. Biol. V. 402 524 2010
PubMed-ID: 20691189  |  Reference-DOI: 10.1016/J.JMB.2010.07.050

(-) Compounds

Molecule 1 - PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET DERIVATIVE
    Expression System Strain: BL21(DE3) DERIVATIVE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TBD_1265
    Organism Scientific: THIOBACILLUS DENITRIFICANS
    Organism Taxid: 292415
    Strain: ATCC 25259

 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
1C2E2Ligand/Ion9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)
2CL1Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION
4MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , HOH A:4 , HOH A:53 , HOH A:84 , HOH A:111 , HOH A:219 , GLN A:509 , GLU A:523 , LEU A:525 , VAL A:526 , ARG A:527 , MSE A:537 , PRO A:538 , VAL A:558 , ARG A:567 , ASN A:584 , ASP A:646 , ASP A:647 , GLN A:670 , GLU A:703 , GLY A:704 , GLU A:706 , GLY A:724 , ASN A:725 , PRO A:730 , MG A:802 , MG A:803BINDING SITE FOR RESIDUE C2E A 801
2AC2SOFTWAREHOH A:1 , GLU A:523 , ASN A:584 , GLU A:616 , ASP A:646 , C2E A:801BINDING SITE FOR RESIDUE MG A 802
3AC3SOFTWAREHOH A:24 , ASP A:646 , ASP A:647 , GLU A:703 , C2E A:801BINDING SITE FOR RESIDUE MG A 803
4AC4SOFTWAREMSE A:537 , ARG A:609BINDING SITE FOR RESIDUE CL A 804
5AC5SOFTWAREHOH B:115 , HOH B:152 , HOH B:157 , HOH B:172 , HOH B:209 , GLN B:509 , GLU B:523 , VAL B:526 , ARG B:527 , PRO B:538 , ILE B:551 , VAL B:558 , ASN B:584 , ASP B:646 , ASP B:647 , GLN B:670 , GLU B:703 , GLY B:704 , ILE B:705 , GLU B:706 , GLY B:724 , ASN B:725 , PRO B:730 , MG B:802 , MG B:803BINDING SITE FOR RESIDUE C2E B 801
6AC6SOFTWAREHOH B:209 , GLU B:523 , ASN B:584 , GLU B:616 , ASP B:646 , C2E B:801BINDING SITE FOR RESIDUE MG B 802
7AC7SOFTWAREHOH B:206 , HOH B:209 , ASP B:646 , ASP B:647 , GLU B:703 , C2E B:801BINDING SITE FOR RESIDUE MG B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N3T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:676 -Pro A:677
2Ile B:676 -Pro B:677

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N3T)

(-) Exons   (0, 0)

(no "Exon" information available for 3N3T)

(-) 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 Q3SJE6_THIDA | Q3SJE6 from UniProtKB/TrEMBL  Length:758

    Alignment length:260
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746
         Q3SJE6_THIDA   487 ERLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVMPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVMLVMTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADAFASLLDRQKAS 746
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeehhhhhh....hhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh...eee.......eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3t A 487 ERLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVmPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVmLVmTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGmEVVAEGIETAQQYAFLRDRGCEFGQGNLmSTPQAADAFASLLDRQKAS 746
                                   496       506       516       526       536|      546       556       566       576       586       596       606       616     | 626       636       646       656       666       676       686       696 |     706       716       726|      736       746
                                                                            537-MSE                                                                              622-MSE                                                                     698-MSE                      727-MSE               
                                                                                                                                                                    625-MSE                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with Q3SJE6_THIDA | Q3SJE6 from UniProtKB/TrEMBL  Length:758

    Alignment length:261
                                   495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745 
         Q3SJE6_THIDA   486 VERLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVMPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVMLVMTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADAFASLLDRQKAS 746
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------EAL-3n3tB01 B:492-730                                                                                                                                                                                                                          ---------------- Pfam domains (1)
           Pfam domains (2) ------EAL-3n3tB02 B:492-730                                                                                                                                                                                                                          ---------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeehhhhhh....hhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh...eee.......eehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3t B 486 HERLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVmPSAFIPAAEDTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARSGLRPDCLELEITENVmLVmTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGLKIDQSFVRKIPAHPSETQIVTTILALARGLGmEVVAEGIETAQQYAFLRDRGCEFGQGNLmSTPQAADAFASLLDRQKAS 746
                                   495       505       515       525       535 |     545       555       565       575       585       595       605       615      |625       635       645       655       665       675       685       695  |    705       715       725 |     735       745 
                                                                             537-MSE                                                                              622-MSE                                                                     698-MSE                      727-MSE               
                                                                                                                                                                     625-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3N3T)

(-) CATH Domains  (0, 0 ; only for superseded entry 3II8: 1,2)

(no "CATH Domain" information available for 3N3T, only for superseded entry 3II8 replaced by 3N3T)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3SJE6_THIDA | Q3SJE6)
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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    Ile A:676 - Pro A:677   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q3SJE6_THIDA | Q3SJE6: 2r6o

(-) Related Entries Specified in the PDB File

2r6o APO-PROTEIN RELATED ID: APC7542 RELATED DB: TARGETDB