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(-) Description

Title :  GTP CYCLOHYDROLASE III FROM M. JANNASCHII (MJ0145) COMPLEXED WITH GTP AND METAL IONS
 
Authors :  S. A. Roberts, V. Bandarian
Date :  07 Aug 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Enzyme, Gtp, Fapy, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Morrison, S. A. Roberts, A. M. Zegeer, W. R. Montfort, V. Bandarian
A New Use For A Familiar Fold: The X-Ray Crystal Structure Of Gtp-Bound Gtp Cyclohydrolase Iii From Methanocaldococcus Jannaschii Reveals A Two Metal Ion Catalytic Mechanism
Biochemistry V. 47 230 2008
PubMed-ID: 18052207  |  Reference-DOI: 10.1021/BI701782E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTP CYCLOHYDROLASE III
    Chains: A, B, C, D
    EC Number: 3.5.4.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GCH3
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: MJ0145;
MJGC

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3K4Ligand/IonPOTASSIUM ION
4NA4Ligand/IonSODIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:230 , GTP A:300 , ARG C:22 , GLU C:24 , HOH C:348BINDING SITE FOR RESIDUE K A 301
02AC2SOFTWAREASP A:138 , ILE A:139 , ASP A:183 , GTP A:300 , NA A:303BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREASP A:138 , ASP A:183 , ASN A:184 , GTP A:300 , CA A:302 , HOH A:332BINDING SITE FOR RESIDUE NA A 303
04AC4SOFTWAREASP B:230 , GTP B:300 , ARG D:22 , GLU D:24 , HOH D:323BINDING SITE FOR RESIDUE K B 301
05AC5SOFTWAREASP B:138 , ILE B:139 , ASP B:183 , GTP B:300 , NA B:303BINDING SITE FOR RESIDUE CA B 302
06AC6SOFTWAREASP B:138 , ASP B:183 , ASN B:184 , GTP B:300 , CA B:302 , HOH B:344BINDING SITE FOR RESIDUE NA B 303
07AC7SOFTWAREARG A:22 , GLU A:24 , ASP C:230 , GTP C:300BINDING SITE FOR RESIDUE K C 301
08AC8SOFTWAREASP C:138 , ILE C:139 , ASP C:183 , GTP C:300 , NA C:303BINDING SITE FOR RESIDUE CA C 302
09AC9SOFTWAREASP C:138 , ASP C:183 , ASN C:184 , GTP C:300 , CA C:302 , HOH C:355BINDING SITE FOR RESIDUE NA C 303
10BC1SOFTWAREARG B:22 , GLU B:24 , HOH B:319 , ASP D:230 , GTP D:300BINDING SITE FOR RESIDUE K D 301
11BC2SOFTWAREASP D:138 , ILE D:139 , ASP D:183 , GTP D:300 , NA D:303BINDING SITE FOR RESIDUE CA D 302
12BC3SOFTWAREASP D:138 , ASP D:183 , ASN D:184 , GTP D:300 , CA D:302 , HOH D:343BINDING SITE FOR RESIDUE NA D 303
13BC4SOFTWAREHIS A:136 , ASP A:138 , ILE A:139 , ASN A:141 , ILE A:142 , THR A:143 , ILE A:180 , GLY A:182 , ASP A:183 , ASN A:184 , LYS A:213 , ARG A:237 , K A:301 , CA A:302 , NA A:303 , HOH A:337 , HOH A:338 , TYR C:12 , THR C:16 , GLU C:24 , LEU C:27 , GLN C:28 , ASP C:55 , GLN C:112 , HOH C:310 , HOH C:327BINDING SITE FOR RESIDUE GTP A 300
14BC5SOFTWAREHIS B:136 , ASP B:138 , ILE B:139 , ASN B:140 , ASN B:141 , ILE B:142 , THR B:143 , ILE B:180 , GLY B:182 , ASP B:183 , ASN B:184 , LYS B:213 , ARG B:237 , K B:301 , CA B:302 , NA B:303 , HOH B:318 , HOH B:344 , HOH B:345 , TYR D:12 , THR D:16 , GLU D:24 , LEU D:27 , GLN D:28 , ASP D:55 , GLN D:112 , HOH D:313BINDING SITE FOR RESIDUE GTP B 300
15BC6SOFTWARETYR A:12 , THR A:16 , GLU A:24 , LEU A:27 , GLN A:28 , ASP A:55 , GLN A:112 , LYS B:206 , HIS C:136 , ASP C:138 , ILE C:139 , ASN C:141 , ILE C:142 , THR C:143 , ILE C:180 , GLY C:182 , ASP C:183 , ASN C:184 , LYS C:213 , ARG C:237 , K C:301 , CA C:302 , NA C:303 , HOH C:304 , HOH C:307 , HOH C:311 , HOH C:329 , HOH C:356BINDING SITE FOR RESIDUE GTP C 300
16BC7SOFTWARELYS A:206 , TYR B:12 , THR B:16 , GLU B:24 , GLN B:28 , ASP B:55 , GLN B:112 , HOH B:319 , HIS D:136 , ASP D:138 , ILE D:139 , ASN D:141 , ILE D:142 , THR D:143 , ILE D:180 , GLY D:182 , ASP D:183 , ASN D:184 , LYS D:213 , ARG D:237 , K D:301 , CA D:302 , NA D:303 , HOH D:308 , HOH D:310 , HOH D:320BINDING SITE FOR RESIDUE GTP D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QV6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:18 -Pro A:19
2Thr B:18 -Pro B:19
3Thr C:18 -Pro C:19
4Thr D:18 -Pro D:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QV6)

(-) Exons   (0, 0)

(no "Exon" information available for 2QV6)

(-) 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:253
 aligned with GCH3_METJA | Q57609 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           GCH3_METJA     1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQDDF 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eee.........eeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeee..eeeee....hhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qv6 A   1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQDDF 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with GCH3_METJA | Q57609 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
           GCH3_METJA     1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQ 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eee.........eeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeee..eeeee....hhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qv6 B   1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQ 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with GCH3_METJA | Q57609 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
           GCH3_METJA     1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQDD 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eee.........eeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeee..eeeee....hhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qv6 C   1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQDD 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  


Chain D from PDB  Type:PROTEIN  Length:253
 aligned with GCH3_METJA | Q57609 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
           GCH3_METJA     1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQDDF 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GGDN-2qv6D01 D:1-250                                                                                                                                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) GGDN-2qv6D02 D:1-250                                                                                                                                                                                                                                      --- Pfam domains (2)
           Pfam domains (3) GGDN-2qv6D03 D:1-250                                                                                                                                                                                                                                      --- Pfam domains (3)
           Pfam domains (4) GGDN-2qv6D04 D:1-250                                                                                                                                                                                                                                      --- Pfam domains (4)
         Sec.struct. author .eeeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhhhh...eee.....eeeee....hhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..........eee.........eeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeee..eeeee....hhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qv6 D   1 MIQITVIQIDNYGPWTVTPNPRRESDLQALQSRLYADLNLMFGAHKGLVFYTRFDNLIAITNGIDLITHKRIQESIRNRYPFTVSMVIASAETPYEAQKLATETLQEYGSAQDENRKEVLDVANELVVDGYVQIAHIDINNITGTLTDIVSAYDTYLNVNKVKLALMEELLKYNALLFFIGGDNFMAPSNGMSEEDFLDIFNRINKKYKIELKAGIGIGRTAEDASNLADIGLEKIRGKLVDKNVCTLKQDDF 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   Legend:   → Mismatch (orange background)
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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 2QV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QV6)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Nucleot_cyclase (14)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GCH3_METJA | Q57609)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0043740    GTP cyclohydrolase IIa activity    Catalysis of the reaction: GTP + 3 H(2)O = 2-amino-5-formylamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + 3 H(+) + 2 phosphate.
    GO:0003933    GTP cyclohydrolase activity    Catalysis of the hydrolysis of the imidazole ring of GTP, releasing formate. Two C-N bonds are hydrolyzed and the pentase unit is isomerized.
    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:0016814    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amidine, a compound of the form R-C(=NH)-NH2.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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  2qv6
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 Related Entries

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