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(-) Description

Title :  CRYSTAL STRUCTURE OF A NUDIX PROTEIN FROM PYROBACULUM AEROPHILUM REVEALS A DIMER WITH INTERTWINED BETA SHEETS
 
Authors :  S. Wang, C. Mura, M. R. Sawaya, D. Cascio, D. Eisenberg
Date :  13 Aug 01  (Deposition) - 03 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Nudix/Mutt-Like Fold, Mixed Alpha/Beta, Tetramerization Due To Hix6X Tag, 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUDIX HOMOLOG
    Chains: A, B, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:145 , GLY C:58 , PHE C:59 , MET C:73 , PRO C:74 , LEU C:75 , TYR D:61 , MET D:73BINDING SITE FOR RESIDUE MPD C 201
2AC2SOFTWARELEU B:8 , VAL B:9 , GLU B:10 , VAL B:98 , LYS B:99 , ARG B:100 , LEU D:149BINDING SITE FOR RESIDUE MPD B 202
3AC3SOFTWAREPHE A:59 , THR A:60 , TYR A:61 , ILE C:142BINDING SITE FOR RESIDUE MPD A 203
4AC4SOFTWARETYR A:61 , GLY B:58 , PHE B:59 , MET B:73 , PRO B:74 , LEU B:75BINDING SITE FOR RESIDUE MPD B 204
5AC5SOFTWAREHIS C:19 , LYS C:20 , GLY C:29 , GLU C:49BINDING SITE FOR RESIDUE MPD C 205
6AC6SOFTWAREGLU C:10 , ASN C:11 , LYS C:13 , ARG C:100 , TRP C:110BINDING SITE FOR RESIDUE MPD C 206

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JRK)

(-) 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:148
 aligned with Q8ZTD8_PYRAE | Q8ZTD8 from UniProtKB/TrEMBL  Length:146

    Alignment length:148
                                                                                                                                                                       146      
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 |      
         Q8ZTD8_PYRAE     5 CIVTSGVLVENGKVLMVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKI------   -
               SCOP domains d1jrka_ A: Hypothetical protein PAE3301                                                                                                              SCOP domains
               CATH domains 1jrkA00 A:1-148 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee......ee..eee.....hhhhhhhhhhhhhhheeeeee......ee..eee.....eeeeeee......eeeeeeeeeeeeeee.....eeee..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrk A   1 MIVTSGVLVENGKVLLVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKISKLAAA 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


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 d1jrkb_ B: Hypothetical protein PAE3301                                                                                                             SCOP domains
               CATH domains 1jrkB00 B:1-147 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.ee..eeeeee......ee..eee.....hhhhhhhhhhhhhhheeeee.......ee..eee.....eeeeeeee....eeeeeeeeeeeeeeee.....eeee..hhhhh...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrk B   1 MIVTSGVLVENGKVLLVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKISKLAA 147
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       


Chain C from PDB  Type:PROTEIN  Length:148
 aligned with Q8ZTD8_PYRAE | Q8ZTD8 from UniProtKB/TrEMBL  Length:146

    Alignment length:148
                                                                                                                                                                       146      
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 |      
         Q8ZTD8_PYRAE     5 CIVTSGVLVENGKVLMVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKI------   -
               SCOP domains d1jrkc_ C: Hypothetical protein PAE3301                                                                                                              SCOP domains
               CATH domains 1jrkC00 C:1-148 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.ee..eeeeee......ee..eee.....hhhhhhhhhhhhhhheeeeee..........eee.....eeeeeeeee..eeeeeeeeeeeeeeeee.....eeee..hhhhh....hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jrk C   1 MIVTSGVLVENGKVLLVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKISKLAAA 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain D 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 d1jrkd_ D: Hypothetical protein PAE3301                                                                                                                SCOP domains
               CATH domains 1jrkD00 D:1-150 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                           CATH domains
           Pfam domains (1) -NUDIX-1jrkD01 D:2-136                                                                                                                  -------------- Pfam domains (1)
           Pfam domains (2) -NUDIX-1jrkD02 D:2-136                                                                                                                  -------------- Pfam domains (2)
           Pfam domains (3) -NUDIX-1jrkD03 D:2-136                                                                                                                  -------------- Pfam domains (3)
           Pfam domains (4) -NUDIX-1jrkD04 D:2-136                                                                                                                  -------------- Pfam domains (4)
         Sec.struct. author .eeeeee.ee..eeeeee......ee..eee.....hhhhhhhhhhhhhhheeeeee......ee..eee.....eeeeeeee....eeeeeeeeeeeeeeee.....eeee..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jrk D   1 MIVTSGVLVENGKVLLVKHKRLGVYIYPGGHVEHNETPIEAVKREFEEETGIVVEPIGFTYGIIDENAVERPMPLVILEEVVKYPEETHIHFDLIYLVKRVGGDLKNGEWIDVREIDRIETFPNVRKVVSLALSTLYRLGKISKLAAALE 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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: 1k26 1k2e

(-) Related Entries Specified in the PDB File

1k26 1K26 CONTAINS THE SAME PROTEIN AS THIS ENTRY, SOLVED BY SAD ON IRIDIUM DERIVATIVE DATA AT 1.85 A RESOLUTION.
1k2e 1K2E CONTAINS THE SAME PROTEIN AS THIS ENTRY, AT 1.8A, SOLVED BY MOLECULAR REPLACEMENT.
1mut NMR STUDY OF MUTT ENZYME, A NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE
1tum MUTT PYROPHOSPHOHYDROLASE-METAL-NUCLEOTIDE-METAL COMPLEX, NMR, 16 STRUCTURES