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(-) Description

Title :  STRUCTURE OF A NUDIX PROTEIN FROM PYROBACULUM AEROPHILUM SOLVED BY THE SINGLE WAVELENGTH ANOMOLOUS SCATTERING METHOD
 
Authors :  S. Wang, C. Mura, M. R. Sawaya, D. Cascio, D. Eisenberg
Date :  26 Sep 01  (Deposition) - 03 Apr 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix/Mutt-Like Fold, Mixed Alpha/Beta, Dimer, Putative Nudix Hydrolase, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wang, C. Mura, M. R. Sawaya, D. Cascio, D. Eisenberg
Structure Of A Nudix Protein From Pyrobaculum Aerophilum Reveals A Dimer With Two Intersubunit Beta-Sheets.
Acta Crystallogr. , Sect. D V. 58 571 2002
PubMed-ID: 11914479  |  Reference-DOI: 10.1107/S0907444902001191

(-) Compounds

Molecule 1 - NUDIX HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B_MUTT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET-22B(+)
    Mutation: YES
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2GOL3Ligand/IonGLYCEROL
3IR34Ligand/IonIRIDIUM (III) ION
4NI2Ligand/IonNICKEL (II) ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:124 , VAL A:125 , ARG A:126 , LYS A:127 , HOH A:236 , HOH A:287BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREASN B:124 , VAL B:125 , ARG B:126 , LYS B:127 , HOH B:234BINDING SITE FOR RESIDUE SO4 B 202
03AC3SOFTWAREHOH A:257 , HOH A:267 , HOH A:270 , HOH A:301 , HOH A:308BINDING SITE FOR RESIDUE IR3 A 203
04AC4SOFTWAREHOH A:287 , LYS B:18 , ASP B:65BINDING SITE FOR RESIDUE IR3 B 204
05AC5SOFTWAREGLU A:66 , HOH A:229BINDING SITE FOR RESIDUE IR3 A 205
06AC6SOFTWARELYS A:20 , HIS A:31 , GOL A:211 , HOH A:256 , HOH A:288BINDING SITE FOR RESIDUE IR3 A 206
07AC7SOFTWAREARG A:21 , TYR A:84 , HIS A:89 , HIS A:91BINDING SITE FOR RESIDUE NI A 207
08AC8SOFTWAREHIS B:31 , HOH B:267 , HOH B:268BINDING SITE FOR RESIDUE NI B 208
09AC9SOFTWAREVAL A:3 , ILE A:26 , GLY A:29 , GLY A:30 , GLU A:80 , HIS A:91 , ASP A:93 , GOL A:211 , HOH A:247 , HOH A:256BINDING SITE FOR RESIDUE GOL A 209
10BC1SOFTWAREMET A:1 , HIS A:89 , ILE A:90 , ARG A:138 , HOH A:264BINDING SITE FOR RESIDUE GOL A 210
11BC2SOFTWAREVAL A:17 , LYS A:18 , HIS A:19 , LYS A:20 , GLY A:29 , GLU A:49 , IR3 A:206 , GOL A:209 , HOH A:256 , HOH A:299BINDING SITE FOR RESIDUE GOL A 211
12BC3SOFTWAREVAL A:81 , LYS A:83 , HOH A:233 , HOH A:259 , HOH B:233BINDING SITE FOR RESIDUE ACY A 212
13BC4SOFTWAREGLU B:80 , ASP B:93 , PRO B:123 , VAL B:125 , HOH B:259BINDING SITE FOR RESIDUE ACY B 213
14BC5SOFTWAREGLU A:10 , ASN A:11BINDING SITE FOR RESIDUE ACY A 214
15BC6SOFTWAREGLU B:10 , ASN B:11 , TRP B:110BINDING SITE FOR RESIDUE ACY B 215
16BC7SOFTWAREGLU B:80 , HIS B:91BINDING SITE FOR RESIDUE ACY B 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K26)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K26)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K26)

(-) Exons   (0, 0)

(no "Exon" information available for 1K26)

(-) 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:150
 aligned with Q8ZTD8_PYRAE | Q8ZTD8 from UniProtKB/TrEMBL  Length:146

    Alignment length:150
                                                                                                                                                                       146        
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 |       -
         Q8ZTD8_PYRAE     5 CIVTSGVLVENGKVLMVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKI--------   -
               SCOP domains d1k26a_ A: Hypothetical protein PAE3301                                                                                                                SCOP domains
               CATH domains 1k26A00 A:1-150 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.ee..eeeeee......ee..eee.....hhhhhhhhhhhhhhheeeeee..........eee.....eeeeeeee....eeeeeeeeeeeeeeee.....eeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1k26 A   1 MIVTSGVLVENGKVLLVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKISKLAAALE 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with Q8ZTD8_PYRAE | Q8ZTD8 from UniProtKB/TrEMBL  Length:146

    Alignment length:147
                                                                                                                                                                       146     
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 |     
         Q8ZTD8_PYRAE     5 CIVTSGVLVENGKVLMVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKI-----   -
               SCOP domains d1k26b_ B: Hypothetical protein PAE3301                                                                                                             SCOP domains
               CATH domains 1k26B00 B:1-147 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                        CATH domains
           Pfam domains (1) -NUDIX-1k26B01 B:2-136                                                                                                                  ----------- Pfam domains (1)
           Pfam domains (2) -NUDIX-1k26B02 B:2-136                                                                                                                  ----------- Pfam domains (2)
         Sec.struct. author .eeeeee.ee..eeeeee......ee..eee.....hhhhhhhhhhhhhhheeeeee......ee..eee.....eeeeeeee....eeeeeeeeeeeeeeee.....eeee..hhhhh....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k26 B   1 MIVTSGVLVENGKVLLVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKISKLAA 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ZTD8_PYRAE | Q8ZTD8)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8ZTD8_PYRAE | Q8ZTD8: 1jrk 1k2e

(-) Related Entries Specified in the PDB File

1jrk 1JRK CONTAINS THE SAME PROTEIN CRYSTALLIZED AS A TETRAMER (DIMER OF DIMERS) IN THE ASYMMETRIC UNIT.
1k2e 1K2E CONTAINS THE SAME PROTEIN AT 1.8A, SOLVED BY MOLECULAR REPLACEMENT.