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(-) Description

Title :  CRYSTAL STRUCTURE OF ADP COMPOUNDS HYDROLASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - ADP COMPOUNDS HYDROLASE NUDE
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NUDE, B3397
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , TYR A:39 , GLU A:40 , SER A:118 , TYR A:119 , HOH A:327 , LEU B:21 , VAL B:68 , ASP B:140 , GLU B:141 , PRO B:142 , HOH B:252 , HOH B:305BINDING SITE FOR RESIDUE APR A 197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VHZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VHZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VHZ)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUDE_ECOLI45-172
 		  2A:45-172
B:45-172
2NUDIX_BOXPS00893 Nudix box signature.NUDE_ECOLI80-101
 		  2A:80-101
B:80-101

(-) Exons   (0, 0)

(no "Exon" information available for 1VHZ)

(-) 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:186
 aligned with NUDE_ECOLI | P45799 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:186
                             1                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      
           NUDE_ECOLI     - -MSKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGR 185
               SCOP domains d1vhza_ A: ADP compounds hydrolase NudE                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeeee....eeeeeeee.....eeeeeee......eeeeeeee..eeeeeeeee....eeeee.eeee.....hhhhhhhhhhhhhhheeeeeeeeeeeee........eeeeeeeeeeee............eeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------NUDIX  PDB: A:45-172 UniProt: 45-172                                                                                            ------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhz A   0 SLSKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGR 185
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with NUDE_ECOLI | P45799 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           NUDE_ECOLI     2 SKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGRV 186
               SCOP domains d1vhzb_ B: ADP compounds hydrolase NudE                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------NUDIX-1vhzB01 B:46-175                                                                                                            ----------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------NUDIX-1vhzB02 B:46-175                                                                                                            ----------- Pfam domains (2)
         Sec.struct. author .......eeeeeeeeee....eeeeeeee.....eeeeeee.....eeeeeeeee..eeeeeeeee....eeeee.eeee.....hhhhhhhhhhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee............eeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------NUDIX  PDB: B:45-172 UniProt: 45-172                                                                                            -------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhz B   2 SKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGRV 186
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VHZ)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NUDE_ECOLI | P45799)
molecular function
    GO:0019144    ADP-sugar diphosphatase activity    Catalysis of the reaction: ADP-sugar + H2O = AMP + sugar 1-phosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1vhz
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  3.6.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUDE_ECOLI | P45799: 1vhg

(-) Related Entries Specified in the PDB File

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