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(-) Description

Title :  METALLO-ENZYME FROM P. MARINA
 
Authors :  D. Bellini, M. A. Walsh, Oxford Protein Production Facility (Oppf
Date :  23 Aug 13  (Deposition) - 19 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Oxford Protein Production Facility, Oppf, Phosphohydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Bellini, D. L. Caly, Y. Mccarthy, M. Bumann, S. Q. An, J. M. Dow, R. P. Ryan, M. A. Walsh
Crystal Structure Of An Hd-Gyp Domain Cyclic-Di-Gmp Phosphodiesterase Reveals An Enzyme With A Novel Trinuclear Catalytic Iron Centre.
Mol. Microbiol. V. 91 26 2014
PubMed-ID: 24176013  |  Reference-DOI: 10.1111/MMI.12447

(-) Compounds

Molecule 1 - METAL DEPENDENT PHOSPHOHYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PERMA_0986
    Mutation: YES
    Organism Scientific: PERSEPHONELLA MARINA
    Organism Taxid: 123214
    Strain: DSM 14350 / EX-H1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1C2E1Ligand/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)
2FE4Ligand/IonFE (III) ION
3SIN5Ligand/IonSUCCINIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:222 , HIS A:250 , HIS A:276 , HIS A:277 , FE A:402 , SIN A:404 , HOH A:501BINDING SITE FOR RESIDUE FE A 401
02AC2SOFTWAREGLU A:185 , ASP A:222 , LYS A:225 , FE A:401 , FE A:403 , SIN A:404 , SIN A:405 , HOH A:501BINDING SITE FOR RESIDUE FE A 402
03AC3SOFTWAREGLU A:185 , HIS A:189 , HIS A:221 , ASP A:222 , ASP A:305 , FE A:402 , SIN A:405 , HOH A:508BINDING SITE FOR RESIDUE FE A 403
04AC4SOFTWAREASP A:222 , LYS A:225 , LYS A:238 , HIS A:250 , HIS A:277 , TYR A:285 , FE A:401 , FE A:402 , HOH A:501 , HOH A:509BINDING SITE FOR RESIDUE SIN A 404
05AC5SOFTWAREGLU A:185 , LYS A:238 , ASP A:305 , ALA A:309 , FE A:402 , FE A:403 , HOH A:501 , HOH A:506 , HOH A:507 , HOH A:510BINDING SITE FOR RESIDUE SIN A 405
06AC6SOFTWARESER A:176 , HIS A:177 , THR A:179 , LYS A:180 , ASP A:183 , GLU A:185 , ILE A:190 , ASP A:222 , HOH A:503 , HOH A:504 , HOH A:508 , HOH A:511BINDING SITE FOR RESIDUE SIN A 406
07AC7SOFTWAREGLU A:275 , GLU A:278 , TRP A:280 , ILE A:294 , GLY A:298 , ARG A:299 , SER A:302 , HIS A:336 , PHE A:337 , ASP A:338BINDING SITE FOR RESIDUE SIN A 407
08AC8SOFTWARELYS A:182 , LYS A:225 , VAL A:226 , ASP A:230 , HOH A:530 , HOH A:531 , LYS B:182 , LYS B:225 , VAL B:226 , LEU B:233 , HOH B:536 , HOH B:541BINDING SITE FOR RESIDUE SIN A 408
09AC9SOFTWAREASP B:222 , HIS B:250 , HIS B:276 , HIS B:277 , HOH B:546BINDING SITE FOR RESIDUE FE B 401
10BC1SOFTWARELYS B:235 , GLY B:237 , LEU B:239 , TRP B:244 , HIS B:277 , TYR B:285 , ASP B:305 , ALA B:309 , LEU B:310 , ARG B:314 , PHE B:328 , HIS B:336 , HOH B:502 , HOH B:504 , HOH B:511BINDING SITE FOR RESIDUE C2E B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:0 -Pro A:1
2Tyr A:285 -Pro A:286
3Tyr B:285 -Pro B:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MDZ)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eeeeeeeeee....eeee........eee...hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdz A   0 DPERKLKILLDYSSKIANEKDLRNVLLFLTDLAKEIMEADRASIFLYDDQKKTLWTIVAHGVDRIEIDADKGIAGYVFRTGEILNIPDAYKDPRFDRDIDKRTGYRTRTILAVPLFDRKQNIIGVFQVINKLTNSVFTEEDIELLRHISLYASSTIENAILYEKLKKAHEDVIYRLSHATKFKDPETQNHIIRVGLYAEILAREAGLDEEDVELVKLAAPMHDIGKVGIPDRVLLKPGKLNDEEWEIMKKHTIYGYEILKGGDSRLLQIAADIAIEHHERWDGTGYPFGKKGEEISIYGRMTSISDVFDALTSDRPYKKAWDMDRTVRFFKEQKGKHFDPFLTDIFLKNIDQMFSIKRELR 360
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359 


Chain B from PDB  Type:PROTEIN  Length:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhheeeeeeeeee....eeee........eee...hhhhhhhhhhh..eee.hhhhh....hhhhhhh......eeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdz B  -2 YQDPERKLKILLDYSSKIANEKDLRNVLLFLTDLAKEIMEADRASIFLYDDQKKTLWTIVAHGVDRIEIDADKGIAGYVFRTGEILNIPDAYKDPRFDRDIDKRTGYRTRTILAVPLFDRKQNIIGVFQVINKLTNSVFTEEDIELLRHISLYASSTIENAILYEKLKKAHEDVIYRLSHATKFKDPETQNHIIRVGLYAEILAREAGLDEEDVELVKLAAPMHDIGKVGIPDRVLLKPGKLNDEEWEIMKKHTIYGYEILKGGDSRLLQIAADIAIEHHERWDGTGYPFGKKGEEISIYGRMTSISDVFDALTSDRPYKKAWDMDRTVRFFKEQKGKHFDPFLTDIFLKNIDQMFSIKRELR 360
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
   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 4MDZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:0 - Pro A:1   [ RasMol ]  
    Tyr A:285 - Pro A:286   [ RasMol ]  
    Tyr B:285 - Pro B:286   [ RasMol ]  
 

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 Related Entries

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UniProtKB/TrEMBL
        C0QQ26_PERMH | C0QQ26: 4mcw 4me4

(-) Related Entries Specified in the PDB File

4mcw A HIGHER RESOLUTION APO STRUCTURE
4me4