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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC PHOSPHODIESTERASE YAHA IN COMPLEX WITH ACTIVATING COFACTOR MG++
 
Authors :  A. Sundriyal, T. Schirmer
Date :  31 Jul 13  (Deposition) - 29 Jan 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
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, C, D
    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: B0315, JW0307, YAHA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2HB04Ligand/IonTRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2HB02Ligand/IonTRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2HB02Ligand/IonTRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2HB02Ligand/IonTRANS-4-(HYDROXYMETHYL)CYCLOHEXANOL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:141 , ASN A:200 , GLU A:232 , ASP A:262 , HOH A:505 , HOH A:515BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWAREVAL A:129 , THR A:138 , GLY A:139 , HIS A:196 , VAL A:230 , GLU A:232 , PHE A:337BINDING SITE FOR RESIDUE HB0 A 402
03AC3SOFTWAREGLY A:265 , ALA A:269 , THR A:270 , TYR A:271 , GLY B:265 , ALA B:269 , THR B:270 , TYR B:271BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWARETHR A:234 , PRO A:238 , ILE A:239 , LEU A:261 , TYR A:273BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREGLU B:141 , ASN B:200 , GLU B:232 , ASP B:262 , HOH B:503 , HOH B:532BINDING SITE FOR RESIDUE MG B 401
06AC6SOFTWAREVAL B:129 , THR B:138 , GLY B:139 , HIS B:196 , VAL B:230 , GLU B:232 , PHE B:337BINDING SITE FOR RESIDUE HB0 B 402
07AC7SOFTWARELEU B:233 , THR B:234 , PRO B:238 , ILE B:239 , LEU B:261 , TYR B:268 , ALA B:269 , TYR B:273BINDING SITE FOR RESIDUE EDO B 403
08AC8SOFTWAREGLU C:141 , ASN C:200 , GLU C:232 , ASP C:262 , HOH C:504 , HOH C:506BINDING SITE FOR RESIDUE MG C 401
09AC9SOFTWAREVAL C:129 , THR C:138 , GLY C:139 , HIS C:196 , VAL C:230 , GLU C:232 , PHE C:281 , VAL C:317 , PHE C:337BINDING SITE FOR RESIDUE HB0 C 402
10BC1SOFTWAREGLY C:265 , ALA C:269 , THR C:270 , TYR C:271 , GLY D:265 , ALA D:269 , THR D:270 , TYR D:271BINDING SITE FOR RESIDUE EDO C 403
11BC2SOFTWAREGLU D:141 , ASN D:200 , GLU D:232 , ASP D:262 , HOH D:503 , HOH D:504BINDING SITE FOR RESIDUE MG D 401
12BC3SOFTWAREVAL D:129 , THR D:138 , GLY D:139 , HIS D:196 , VAL D:230 , GLU D:232 , LYS D:283 , VAL D:317 , PHE D:337BINDING SITE FOR RESIDUE HB0 D 402
13BC4SOFTWARELEU D:233 , THR D:234 , ILE D:239 , TYR D:273 , HOH D:506 , HOH D:507BINDING SITE FOR RESIDUE EDO D 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LYK)

(-) Sequences/Alignments

Asymmetric 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhh...eeeehhhhhhhh....hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...ee........eehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyk A 107 IVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVMK 359
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh..hhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhh...eeeehhhhhh......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...ee........eehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyk B 107 IVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVMK 359
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   


Chain C from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhh...eeeehhhhhh......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...ee........eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lyk C 107 IVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVM 358
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356  


Chain D from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..eeeeeeeeee.....eeeeeeeeeeee...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhh.hhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhh...eeeehhhhhh......hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...ee........eehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lyk D 106 HIVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVM 358
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
   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 4LYK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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 Related Entries

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

UniProtKB/Swiss-Prot
        YAHA_ECOLI | P21514: 4kie 4lj3

(-) Related Entries Specified in the PDB File

4kie CRYSTAL STRUCTURE OF THE EAL DOMAIN OF C-DI-GMP SPECIFIC PHOSPHODIESTERASE YAHA
4lj3