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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC PHOSPHODIESTERASE YAHA IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CA++
 
Authors :  A. Sundriyal, T. Schirmer
Date :  04 Jul 13  (Deposition) - 29 Jan 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pgpg, Phosphodiesterase, Tim-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sundriyal, C. Massa, D. Samoray, F. Zehender, T. Sharpe, U. Jenal, T. Schirmer
Inherent Regulation Of Eal Domain-Catalyzed Hydrolysis Of Second Messenger Cyclic Di-Gmp.
J. Biol. Chem. V. 289 6978 2014
PubMed-ID: 24451384  |  Reference-DOI: 10.1074/JBC.M113.516195

(-) Compounds

Molecule 1 - CYCLIC DI-GMP PHOSPHODIESTERASE YAHA
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EAL DOMAIN CONTAINING RESIDUES 101-362
    Gene: YAHA, B0315, JW0307
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
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)
2CA4Ligand/IonCALCIUM ION
3HB02Ligand/IonTRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL
4IMD2Ligand/IonIMIDAZOLE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:127 , GLU A:141 , LEU A:143 , VAL A:144 , ARG A:145 , PRO A:156 , ILE A:169 , LEU A:176 , ASN A:200 , ASP A:262 , ASP A:263 , LYS A:286 , GLU A:319 , GLY A:320 , VAL A:321 , GLU A:322 , GLY A:340 , TYR A:341 , PRO A:346 , CA A:402 , CA A:403 , IMD A:404 , HOH A:504 , HOH A:507 , HOH A:512 , HOH A:521 , HOH A:574 , HOH A:583 , HOH A:586 , HOH A:653 , HOH A:685 , HOH A:693 , HOH A:695BINDING SITE FOR RESIDUE C2E A 401
02AC2SOFTWAREGLU A:141 , ASN A:200 , GLU A:232 , ASP A:262 , C2E A:401 , HOH A:505BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREASP A:263 , GLU A:319 , C2E A:401 , HOH A:506 , HOH A:520 , HOH A:586BINDING SITE FOR RESIDUE CA A 403
04AC4SOFTWAREASN A:200 , VAL A:201 , GLU A:232 , THR A:234 , ASP A:262 , C2E A:401 , HOH A:588BINDING SITE FOR RESIDUE IMD A 404
05AC5SOFTWAREVAL A:129 , THR A:138 , GLY A:139 , CYS A:140 , HIS A:196 , VAL A:230 , GLU A:232 , VAL A:317 , PHE A:337BINDING SITE FOR RESIDUE HB0 A 405
06AC6SOFTWAREGLN B:127 , GLU B:141 , LEU B:143 , VAL B:144 , ARG B:145 , PRO B:156 , GLU B:164 , LEU B:176 , ASN B:200 , ASP B:262 , ASP B:263 , LYS B:286 , GLU B:319 , GLY B:320 , VAL B:321 , GLU B:322 , GLY B:340 , TYR B:341 , PRO B:346 , CA B:402 , CA B:403 , IMD B:404 , HOH B:501 , HOH B:506 , HOH B:510 , HOH B:514 , HOH B:561 , HOH B:575BINDING SITE FOR RESIDUE C2E B 401
07AC7SOFTWAREGLU B:141 , ASN B:200 , GLU B:232 , ASP B:262 , C2E B:401 , HOH B:503BINDING SITE FOR RESIDUE CA B 402
08AC8SOFTWAREASP B:263 , ASP B:285 , GLU B:319 , C2E B:401 , HOH B:505 , HOH B:553BINDING SITE FOR RESIDUE CA B 403
09AC9SOFTWAREASN B:200 , VAL B:201 , GLU B:232 , THR B:234 , ASP B:262 , C2E B:401 , HOH B:658BINDING SITE FOR RESIDUE IMD B 404
10BC1SOFTWAREVAL B:129 , THR B:138 , GLY B:139 , HIS B:196 , VAL B:230 , GLU B:232 , VAL B:317 , PHE B:337BINDING SITE FOR RESIDUE HB0 B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LJ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LJ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LJ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LJ3)

(-) Exons   (0, 0)

(no "Exon" information available for 4LJ3)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhh.hhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh...eeeehhhhhh......hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eee.......eehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lj3 A 104 YHHIVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVMK 359
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353      


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhh.hhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh...eeeehhhhhh......hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eee.......eehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lj3 B 104 YHHIVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVMK 359
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   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 4LJ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LJ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LJ3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        YAHA_ECOLI | P21514: 4kie 4lyk

(-) Related Entries Specified in the PDB File

4kie CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC PHOSPHODIESTERASE YAHA
4lyk