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(-) Description

Title :  STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH MG AND DUMP
 
Authors :  A. M. D. Goncalves, D. De Sanctis, S. M. Mcsweeney
Date :  05 Apr 11  (Deposition) - 06 Jul 11  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hydrolase, Dimeric Dutpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. D. Goncalves, D. Desanctis, S. M. Mcsweeney
Structural And Functional Insights Into Dr2231 Protein, The Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans.
J. Biol. Chem. V. 286 30691 2011
PubMed-ID: 21733847  |  Reference-DOI: 10.1074/JBC.M111.247999

(-) Compounds

Molecule 1 - MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
    Chains: A, B, C, D
    EC Number: 3.6.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D-TOPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1
    Synonym: DR2231

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:47 , GLU A:50 , GLU A:79 , ASP A:82BINDING SITE FOR RESIDUE MG A1146
02AC2SOFTWAREVAL A:105 , ASN A:109 , LYS A:112 , LYS A:122 , GLN A:123 , LYS A:125 , HOH A:2076 , HOH A:2096 , HOH A:2097 , HOH A:2098 , HOH A:2099 , HOH A:2100 , HOH A:2101 , HOH A:2102 , PHE B:17 , GLU B:47 , ASP B:82 , TYR B:85 , VAL B:86 , HOH B:2048BINDING SITE FOR RESIDUE UMP A1147
03AC3SOFTWAREHIS A:18 , ARG A:40 , HOH A:2024BINDING SITE FOR RESIDUE CL A1148
04AC4SOFTWAREGLU B:47 , GLU B:50 , GLU B:79 , ASP B:82 , HOH B:2048BINDING SITE FOR RESIDUE MG B1145
05AC5SOFTWAREALA A:132 , VAL A:134 , HIS B:78BINDING SITE FOR RESIDUE ACT B1146
06AC6SOFTWAREGLU C:47 , GLU C:50 , GLU C:79 , ASP C:82 , HOH C:2043BINDING SITE FOR RESIDUE MG C1144
07AC7SOFTWAREVAL C:105 , ASN C:109 , LYS C:112 , LYS C:122 , GLN C:123 , LYS C:125 , HOH C:2091 , HOH C:2092 , HOH C:2093 , HOH C:2094 , HOH C:2095 , HOH C:2096 , HOH C:2097 , PHE D:17 , GLU D:47 , ASP D:82 , TYR D:85 , VAL D:86 , HOH D:2042BINDING SITE FOR RESIDUE UMP C1145
08AC8SOFTWAREGLU D:47 , GLU D:50 , GLU D:79 , ASP D:82 , HOH D:2042BINDING SITE FOR RESIDUE MG D1145
09AC9SOFTWAREALA A:119 , HOH A:2032 , HOH A:2080 , ALA D:24 , GLN D:93 , HOH D:2072BINDING SITE FOR RESIDUE CL D1146
10BC1SOFTWARELYS A:125 , ARG D:61 , GLU D:66 , ALA D:67 , ASP D:72 , HOH D:2065 , HOH D:2086BINDING SITE FOR RESIDUE GOL D1147
11BC2SOFTWAREALA C:132 , VAL C:134 , ALA D:74 , HIS D:78BINDING SITE FOR RESIDUE ACT D1148

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1C:6 -D:6

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:144 -Pro A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YFD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YFD)

(-) Exons   (0, 0)

(no "Exon" information available for 2YFD)

(-) 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:138
 aligned with Q9RS96_DEIRA | Q9RS96 from UniProtKB/TrEMBL  Length:148

    Alignment length:139
                                    16        26        36        46        56        66        76        86        96       106       116       126       136         
         Q9RS96_DEIRA     7 PPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHAP 145
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..-........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....................hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yfd A   7 PPTNAERLHEFHRAIGA-TPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHAP 145
                                    16      | 26        36        46        56        66        76        86        96       106       116       126       136         
                                           23 |                                                                                                                        
                                             25                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with Q9RS96_DEIRA | Q9RS96 from UniProtKB/TrEMBL  Length:148

    Alignment length:138
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        
         Q9RS96_DEIRA     7 PPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHA 144
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.--------.........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yfd B   7 PPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASG--------LKPEGWRPADVRGVIERLQHA 144
                                    16        26        36        46        56        66        76        86        96       106        |-       126       136        
                                                                                                                                      115      124                    


Chain C from PDB  Type:PROTEIN  Length:137
 aligned with Q9RS96_DEIRA | Q9RS96 from UniProtKB/TrEMBL  Length:148

    Alignment length:138
                                    15        25        35        45        55        65        75        85        95       105       115       125       135        
         Q9RS96_DEIRA     6 CPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQH 143
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..-........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yfd C   6 CPPTNAERLHEFHRAIGA-TPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQH 143
                                    15       |25        35        45        55        65        75        85        95       105       115       125       135        
                                            23 |                                                                                                                      
                                              25                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:130
 aligned with Q9RS96_DEIRA | Q9RS96 from UniProtKB/TrEMBL  Length:148

    Alignment length:139
                                    15        25        35        45        55        65        75        85        95       105       115       125       135         
         Q9RS96_DEIRA     6 CPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHA 144
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------PRA-PH-2yfdD01 D:14-109                                                                         ----------------------------------- Pfam domains (1)
           Pfam domains (2) --------PRA-PH-2yfdD02 D:14-109                                                                         ----------------------------------- Pfam domains (2)
           Pfam domains (3) --------PRA-PH-2yfdD03 D:14-109                                                                         ----------------------------------- Pfam domains (3)
           Pfam domains (4) --------PRA-PH-2yfdD04 D:14-109                                                                         ----------------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.---------........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yfd D   6 CPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEESAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASG---------KPEGWRPADVRGVIERLQHA 144
                                    15        25        35        45        55        65        75        85        95       105       115       125       135         
                                                                                                                                       115       125
   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 2YFD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YFD)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9RS96_DEIRA | Q9RS96)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047429    nucleoside-triphosphate diphosphatase activity    Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.

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  2yfd
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  3.6.1.19
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 Related Entries

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

UniProtKB/TrEMBL
        Q9RS96_DEIRA | Q9RS96: 2yeu 2yf3 2yf4 2yf9 2yfc 5hva 5hwu 5hx1 5hyl 5hzz 5i0j 5i0m

(-) Related Entries Specified in the PDB File

2yeu STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEX WITH GD
2yf3 CRYSTAL STRUCTURE OF DR2231, THE MAZG-LIKE PROTEIN FROM DEINOCOCCUS RADIODURANS, COMPLEX WITH MANGANESE
2yf4 CRYSTAL STRUCTURE OF DR2231, THE MAZG-LIKE PROTEIN FROM DEINOCOCCUS RADIODURANS, APO STRUCTURE
2yf9 STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, NATIVE FORM
2yfc STRUCTURAL AND FUNCTIONAL INSIGHTS OF DR2231 PROTEIN, THE MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM DEINOCOCCUS RADIODURANS, COMPLEXED WITH MN AND DUMP