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(-) Description

Title :  CRYSTAL STRUCTURE OF PURO/IMP FROM METHANOTHERMOBACTER THERMOAUTOTROPHICUS
 
Authors :  Y. N. Kang, A. Tran, R. H. White, S. E. Ealick
Date :  07 Nov 06  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha-Beta-Beta-Alpha Ntn Hydrolase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. N. Kang, A. Tran, R. H. White, S. E. Ealick
A Novel Function For The N-Terminal Nucleophile Hydrolase Fold Demonstrated By The Structure Of An Archaeal Inosine Monophosphate Cyclohydrolase.
Biochemistry V. 46 5050 2007
PubMed-ID: 17407260  |  Reference-DOI: 10.1021/BI061637J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMP CYCLOHYDROLASE
    Chains: A, B, C, D
    EC Number: 3.5.4.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PURO
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262
    Synonym: INOSINICASE, IMP SYNTHETASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1IMP4Ligand/IonINOSINIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:2 , ARG A:5 , SER A:24 , ARG A:25 , SER A:26 , ARG A:30 , ASN A:54 , TYR A:56 , TYR A:59 , ASN A:73 , GLU A:104 , ASP A:106 , THR A:110 , TYR A:148BINDING SITE FOR RESIDUE IMP A 205
2AC2SOFTWARETYR B:2 , ARG B:5 , SER B:24 , ARG B:25 , SER B:26 , ARG B:30 , ASN B:54 , TYR B:56 , TYR B:59 , ASN B:73 , GLU B:104 , ASP B:106 , THR B:110 , TYR B:148 , HOH B:371BINDING SITE FOR RESIDUE IMP B 206
3AC3SOFTWARETYR C:2 , ARG C:5 , SER C:24 , ARG C:25 , SER C:26 , ARG C:30 , ASN C:54 , TYR C:56 , TYR C:59 , ASN C:73 , GLU C:104 , ASP C:106 , THR C:110 , TYR C:148 , HOH C:315BINDING SITE FOR RESIDUE IMP C 207
4AC4SOFTWARETYR D:2 , ARG D:5 , SER D:24 , ARG D:25 , SER D:26 , ARG D:30 , ASN D:54 , TYR D:56 , TYR D:59 , ASN D:73 , GLU D:104 , ASP D:106 , THR D:110 , TYR D:148 , HOH D:300 , HOH D:489BINDING SITE FOR RESIDUE IMP D 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NTK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NTK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NTK)

(-) 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:206
 aligned with PURO_METTH | O27099 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:206
                                1                                                                                                                                                                                                         
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196      
           PURO_METTH     - ----MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
               SCOP domains d2ntka_ A: Hypothetical protein MTH1020                                                                                                                                                                        SCOP domains
               CATH domains 2ntkA00 A:-3-202 Hypothetical protein MTH1020                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee..eeeeeeeee......eeeeee..eeeeee...hhhhhhh.....eeeeeee..eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhh.........eeeeee....eeeeeee..eeeeee......eeee.......ee......hhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntk A  -3 RGSHMYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196      


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with PURO_METTH | O27099 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           PURO_METTH     1 MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
               SCOP domains d2ntkb_ B: Hypothetical protein MTH1020                                                                                                                                                                    SCOP domains
               CATH domains 2ntkB00 B:1-202 Hypothetical protein MTH1020                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..eeeeeeeee......eeeeee..eeeeee...hhhhhhh.....eeeeeee..eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhh.........eeeeee....eeeeeee..eeeeee......eeee.......ee......hhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntk B   1 MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain C from PDB  Type:PROTEIN  Length:202
 aligned with PURO_METTH | O27099 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           PURO_METTH     1 MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
               SCOP domains d2ntkc_ C: Hypothetical protein MTH1020                                                                                                                                                                    SCOP domains
               CATH domains 2ntkC00 C:1-202 Hypothetical protein MTH1020                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..eeeeeeeee......eeeeee..eeeeee...hhhhhhh.....eeeeeee..eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhh.........eeeeee....eeeeeee..eeeeee......eeee.......ee......hhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntk C   1 MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain D from PDB  Type:PROTEIN  Length:202
 aligned with PURO_METTH | O27099 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           PURO_METTH     1 MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
               SCOP domains d2ntkd_ D: Hypothetical protein MTH1020                                                                                                                                                                    SCOP domains
               CATH domains 2ntkD00 D:1-202 Hypothetical protein MTH1020                                                                                                                                                               CATH domains
           Pfam domains (1) IMP_cyclohyd-2ntkD01 D:1-202                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) IMP_cyclohyd-2ntkD02 D:1-202                                                                                                                                                                               Pfam domains (2)
           Pfam domains (3) IMP_cyclohyd-2ntkD03 D:1-202                                                                                                                                                                               Pfam domains (3)
           Pfam domains (4) IMP_cyclohyd-2ntkD04 D:1-202                                                                                                                                                                               Pfam domains (4)
         Sec.struct. author .....eeeeeee..eeeeeeeee......eeeeee..eeeeee...hhhhhhh.....eeeeeee..eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhh.........eeeeee....eeeeeee..eeeeee......eeee.......ee......hhhhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntk D   1 MYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: IMP_cyclohyd] (3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PURO_METTH | O27099)
molecular function
    GO:0003937    IMP cyclohydrolase activity    Catalysis of the reaction: IMP + H2O = 5-formamido-1-(5-phosphoribosyl)imidazole-4-carboxamide.
    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.
biological process
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0006188    IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PURO_METTH | O27099: 1kuu 2ntl 2ntm

(-) Related Entries Specified in the PDB File

2ntl 2ntm