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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GGDEF DOMAIN FROM MARINOBACTER AQUAEOLEI DIGUANYLATE CYCLASE COMPLEXED WITH C-DI-GMP - NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET MQR89A
 
Authors :  S. Vorobiev, H. Neely, J. Seetharaman, H. Wang, E. L. Foote, C. Ciccosan S. Sahdev, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, No Structural Genomics Consortium (Nesg)
Date :  28 Jul 09  (Deposition) - 11 Aug 09  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A
Keywords :  Diguanylate Cyclase, Ggdef Domain, A1U3W3_marav, Nesg, Mqr89A, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Vorobiev, H. Neely, B. Yu, J. Seetharaman, R. Xiao, T. B. Acton, G. T. Montelione, J. F. Hunt
Crystal Structure Of A Catalytically Active Gg(D/E)Ef Diguanylate Cyclase Domain From Marinobacter Aquaeolei With Bound C-Di-Gmp Product.
J. Struct. Funct. Genom. V. 13 177 2012
PubMed-ID: 22843345  |  Reference-DOI: 10.1007/S10969-012-9136-4

(-) Compounds

Molecule 1 - DIGUANYLATE CYCLASE
    Atcc: 700491/DSM 11845/VT8
    Chains: A
    EC Number: 2.7.7.65
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) +MAGIC
    Expression System Taxid: 562
    Expression System Vector: PET 21-23C
    Fragment: GGDEF DOMAIN
    Gene: MAQU_2607
    Organism Scientific: MARINOBACTER AQUAEOLEI VT8
    Organism Taxid: 351348

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
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)
2MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:182 , TYR A:183 , ASN A:223 , ARG A:225 , ASP A:228 , THR A:245 , SER A:249 , VAL A:252 , ILE A:253 , ARG A:256 , LYS A:304 , C2E A:402 , HOH A:507 , HOH A:520 , HOH A:535 , HOH A:564 , HOH A:612BINDING SITE FOR RESIDUE C2E A 401
2AC2SOFTWAREARG A:182 , ASN A:223 , ILE A:224 , ARG A:225 , GLN A:226 , ARG A:256 , LYS A:304 , GLU A:307 , C2E A:401 , HOH A:527 , HOH A:532 , HOH A:585 , HOH A:602 , HOH A:612 , HOH A:625 , HOH A:657 , HOH A:664BINDING SITE FOR RESIDUE C2E A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IGN)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:166
 aligned with A1U3W3_MARHV | A1U3W3 from UniProtKB/TrEMBL  Length:316

    Alignment length:166
                                                                                                                                                                                              316 
                                   161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    | 
         A1U3W3_MARHV   152 AKLSMTDRLTGLLNRGTWENLVDAEYERFRRYGQATSLVMFDIDHFKPVNDTYGHLAGDEVIRHTADVTRNNIRQSDSAGRYGGEEFGIILPETDAESARVICERIREAIEKSTVSTSAGDIQYTVSMGIAQLTETPENYMQWMQKADEALYKAKESGRNKVVVS-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eehhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee....eeeeeee..hhhhhhhhhhhhhhhhhh..ee....ee...eeeeeee......hhhhhhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ign A 152 AKLSmTDRLTGLLNRGTWENLVDAEYERFRRYGQATSLVmFDIDHFKPVNDTYGHLAGDEVIRHTADVTRNNIRQSDSAGRYGGEEFGIILPETDAESARVICERIREAIEKSTVSTSAGDIQYTVSmGIAQLTETPENYmQWmQKADEALYKAKESGRNKVVVSL 317
                                |  161       171       181       191       201       211       221       231       241       251       261       271       281       291|  |   301       311      
                                |                                191-MSE                                                                                 279-MSE      292-MSE                     
                              156-MSE                                                                                                                                    295-MSE
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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 3IGN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1U3W3_MARHV | A1U3W3)
molecular function
    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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