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(-) Description

Title :  CRYSTAL STRUCTURE OF NUDIX HYDROLASE FROM NITROSOMONAS EUROPAEA
 
Authors :  J. Osipiuk, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak, Center For Structural Genomics (Mcsg)
Date :  25 Mar 08  (Deposition) - 08 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Apc7497, Nudix Hydrolase, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Osipiuk, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Nudix Hydrolase From Nitrosomona Europaea.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUDIX HYDROLASE
    Atcc19718
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneNE1158
    Organism ScientificNITROSOMONAS EUROPAEA ATCC 19718
    Organism Taxid228410
    StrainIFO 14298

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 36)

Asymmetric Unit (6, 36)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL4Ligand/IonGLYCEROL
4MSE16Mod. Amino AcidSELENOMETHIONINE
5NA2Ligand/IonSODIUM ION
6ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE8Mod. Amino AcidSELENOMETHIONINE
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE8Mod. Amino AcidSELENOMETHIONINE
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:4 , CYS A:7 , CYS A:26 , CYS A:29BINDING SITE FOR RESIDUE ZN A 508
02AC2SOFTWARECYS B:4 , CYS B:7 , CYS B:26 , CYS B:29BINDING SITE FOR RESIDUE ZN B 509
03AC3SOFTWARECYS C:4 , CYS C:7 , CYS C:26 , CYS C:29BINDING SITE FOR RESIDUE ZN C 510
04AC4SOFTWARECYS D:4 , CYS D:7 , CYS D:26 , CYS D:29BINDING SITE FOR RESIDUE ZN D 511
05AC5SOFTWAREGLU A:85BINDING SITE FOR RESIDUE NA A 512
06AC6SOFTWAREGLU B:85BINDING SITE FOR RESIDUE NA B 513
07AC7SOFTWAREGLU B:98 , LEU B:99BINDING SITE FOR RESIDUE CL B 514
08AC8SOFTWARETHR D:77 , LEU D:78 , HIS D:164BINDING SITE FOR RESIDUE CL D 515
09AC9SOFTWARETHR C:77 , LEU C:78 , SER D:104BINDING SITE FOR RESIDUE CL C 516
10BC1SOFTWARELEU A:171 , THR B:77 , LEU B:78BINDING SITE FOR RESIDUE CL B 517
11BC2SOFTWARETHR A:77 , LEU A:78BINDING SITE FOR RESIDUE CL A 518
12BC3SOFTWAREARG A:149BINDING SITE FOR RESIDUE CL A 519
13BC4SOFTWAREGLU A:98 , LEU A:99BINDING SITE FOR RESIDUE CL A 520
14BC5SOFTWAREARG A:14 , ARG C:93 , ASP C:123BINDING SITE FOR RESIDUE EDO C 505
15BC6SOFTWAREASN A:36 , PHE B:71BINDING SITE FOR RESIDUE EDO A 506
16BC7SOFTWARETYR D:112BINDING SITE FOR RESIDUE EDO D 507
17BC8SOFTWAREILE A:40 , GLN A:110 , TYR A:112 , PHE A:148BINDING SITE FOR RESIDUE GOL A 501
18BC9SOFTWAREILE B:40 , LEU B:105 , GLN B:110 , TYR B:112 , PHE B:148BINDING SITE FOR RESIDUE GOL B 502
19CC1SOFTWAREILE C:40 , LEU C:105 , ILE C:108 , GLN C:110 , TYR C:112BINDING SITE FOR RESIDUE GOL C 503
20CC2SOFTWAREILE D:40 , LEU D:105 , ILE D:108 , GLN D:110 , TYR D:112 , PHE D:148BINDING SITE FOR RESIDUE GOL D 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:59 -Pro A:60
2Ala B:59 -Pro B:60
3Ala C:59 -Pro C:60
4Ala D:59 -Pro D:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CNG)

(-) 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:177
 aligned with Q82VD6_NITEU | Q82VD6 from UniProtKB/TrEMBL  Length:185

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
         Q82VD6_NITEU     1 MKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFHLGIINKP 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3cngA01 A:2-35                    3cngA02 A:36-177 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee........eeee....eee....eeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeehhh.eeeeeeeeee..........eeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhh....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cng A   1 mKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFmENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYmLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYmEERHHGQPAFHLGIINKP 177
                            |       10        20        30        40        50        60        70 |      80        90       100       110  |    120       130       140       150       160       170       
                            |                                                                     72-MSE                                  113-MSE                                       159-MSE              
                            1-MSE                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q82VD6_NITEU | Q82VD6 from UniProtKB/TrEMBL  Length:185

    Alignment length:176
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
         Q82VD6_NITEU     1 MKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFHLGIINK 176
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3cngB01 B:2-35                    3cngB02 B:36-176 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee........eeee....eee....eeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeehhh.eeeeeeeeee..........eeeeeee.....hhhhh.hhhhhhhhhhhhhhh.......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cng B   1 mKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFmENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYmLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYmEERHHGQPAFHLGIINK 176
                            |       10        20        30        40        50        60        70 |      80        90       100       110  |    120       130       140       150       160       170      
                            1-MSE                                                                 72-MSE                                  113-MSE                                       159-MSE             

Chain C from PDB  Type:PROTEIN  Length:178
 aligned with Q82VD6_NITEU | Q82VD6 from UniProtKB/TrEMBL  Length:185

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
         Q82VD6_NITEU     1 MKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFHLGIINKPQ 178
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3cngC01 C:2-35                    3cngC02 C:36-178 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee........eeee....eee....eeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeehhh.eeeeeeeeee..........eeeeeeehhhhhhhhhh.hhhhhhhhhhhhhhhh......eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cng C   1 mKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFmENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYmLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYmEERHHGQPAFHLGIINKPQ 178
                            |       10        20        30        40        50        60        70 |      80        90       100       110  |    120       130       140       150       160       170        
                            1-MSE                                                                 72-MSE                                  113-MSE                                       159-MSE               

Chain D from PDB  Type:PROTEIN  Length:177
 aligned with Q82VD6_NITEU | Q82VD6 from UniProtKB/TrEMBL  Length:185

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
         Q82VD6_NITEU     1 MKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFHLGIINKP 177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3cngD01 D:2-35                    3cngD02 D:36-177 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee........eeee....eee....eeeeeeeeee..eeeeeee........ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeehhh.eeeeeeeeee..........eeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhh....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cng D   1 mKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFmENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYmLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYmEERHHGQPAFHLGIINKP 177
                            |       10        20        30        40        50        60        70 |      80        90       100       110  |    120       130       140       150       160       170       
                            1-MSE                                                                 72-MSE                                  113-MSE                                       159-MSE              

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  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 3CNG)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q82VD6_NITEU | Q82VD6)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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