1WM9 - JenaLib

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Title :   STRUCTURE OF GTP CYCLOHYDROLASE I FROM THERMUS THERMOPHILUS HB8

Authors :   Y. Tanaka, Riken Structural Genomics/Proteomics Initiative (Rs

Date :   05 Jul 04 (Deposition) - 19 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E  (2x)

Keywords :   Beta Barrel, Hydrolase, Pteridine, Tetrahydrobiopterin, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tanaka, N. Nakagawa, S. Kuramitsu, S. Yokoyama, R. Masui
Novel Reaction Mechanism Of Gtp Cyclohydrolase I. High-Resolution X-Ray Crystallography Of Thermus Thermophilus Hb8 Enzyme Complexed With A Transition State Analogue, The 8-Oxoguanine Derivative.
J. Biochem. (Tokyo) V. 138 263 2005
PubMed-ID: 16169877 | Reference-DOI: 10.1093/JB/MVI120

Molecule 1 - GTP CYCLOHYDROLASE I
	Chains	:	A, B, C, D, E
	EC Number	:	3.5.4.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	ZN	5	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:108 , HIS A:111 , CYS A:179	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS B:108 , HIS B:111 , CYS B:179	BINDING SITE FOR RESIDUE ZN B 1002
3	AC3	SOFTWARE	CYS C:108 , HIS C:111 , CYS C:179 , HOH C:1018	BINDING SITE FOR RESIDUE ZN C 1003
4	AC4	SOFTWARE	CYS D:108 , HIS D:111 , CYS D:179	BINDING SITE FOR RESIDUE ZN D 1004
5	AC5	SOFTWARE	CYS E:108 , HIS E:111 , CYS E:179	BINDING SITE FOR RESIDUE ZN E 1005

(no "SS Bond" information available for 1WM9)

(no "Cis Peptide Bond" information available for 1WM9)

(no "SAP(SNP)/Variant" information available for 1WM9)

(no "PROSITE Motif" information available for 1WM9)

(no "Exon" information available for 1WM9)

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:185
 aligned with Q5SH52_THET8 | Q5SH52 from UniProtKB/TrEMBL  Length:220

    Alignment length:185
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
         Q5SH52_THET8    32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
               SCOP domains d1wm9a1 A:32-216 GTP cyclohydrolase I                                                                                                                                                     SCOP domains
               CATH domains 1wm9A01 A:32-85  [code=1.10.286.10, no name defined]  1wm9A02 A:86-216  [code=3.30.1130.10, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....hhhhhhh..eee......eeeeeeeeeeee.....eeeeeeeeeee...eeehhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhh........eeeeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wm9 A  32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with Q5SH52_THET8 | Q5SH52 from UniProtKB/TrEMBL  Length:220

    Alignment length:185
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
         Q5SH52_THET8    32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
               SCOP domains d1wm9b_ B: GTP cyclohydrolase I                                                                                                                                                           SCOP domains
               CATH domains 1wm9B01 B:32-85  [code=1.10.286.10, no name defined]  1wm9B02 B:86-216  [code=3.30.1130.10, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeeeeeeeeee.....eeeeeeeeeee...eeehhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhh........eeeeeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wm9 B  32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain C from PDB  Type:PROTEIN  Length:185
 aligned with Q5SH52_THET8 | Q5SH52 from UniProtKB/TrEMBL  Length:220

    Alignment length:185
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
         Q5SH52_THET8    32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
               SCOP domains d1wm9c_ C: GTP cyclohydrolase I                                                                                                                                                           SCOP domains
               CATH domains 1wm9C01 C:32-85  [code=1.10.286.10, no name defined]  1wm9C02 C:86-216  [code=3.30.1130.10, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeeeeeeeeee.....eeeeeeeeeee...eeehhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhh........eeeeeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wm9 C  32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain D from PDB  Type:PROTEIN  Length:185
 aligned with Q5SH52_THET8 | Q5SH52 from UniProtKB/TrEMBL  Length:220

    Alignment length:185
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
         Q5SH52_THET8    32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
               SCOP domains d1wm9d_ D: GTP cyclohydrolase I                                                                                                                                                           SCOP domains
               CATH domains 1wm9D01 D:32-85  [code=1.10.286.10, no name defined]  1wm9D02 D:86-216  [code=3.30.1130.10, no name defined]                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeeeeeeeeee.....eeeeeeeeeee...eeehhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh...eeeeeeeeeehhhhh........eeeeeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wm9 D  32 EVDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain E from PDB  Type:PROTEIN  Length:184
 aligned with Q5SH52_THET8 | Q5SH52 from UniProtKB/TrEMBL  Length:220

    Alignment length:184
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
         Q5SH52_THET8    33 VDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
               SCOP domains d1wm9e_ E: GTP cyclohydrolase I                                                                                                                                                          SCOP domains
               CATH domains 1wm9E01 E:33-85  [code=1.10.286.10, no name defined] 1wm9E02 E:86-216  [code=3.30.1130.10, no name defined]                                                                              CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------GTP_cyclohydroI-1wm9E01 E:114-199                                                     ----------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------GTP_cyclohydroI-1wm9E02 E:114-199                                                     ----------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------GTP_cyclohydroI-1wm9E03 E:114-199                                                     ----------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------GTP_cyclohydroI-1wm9E04 E:114-199                                                     ----------------- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------GTP_cyclohydroI-1wm9E05 E:114-199                                                     ----------------- Pfam domains (5)
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee......eeeeeeeeeeee.....eeeeeeeeeee...eeehhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhh........eeeeeeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wm9 E  33 VDLERLQALAAEWLQVIGEDPGREGLLKTPERVAKAWAFLTRGYRQRLEEVVGGAVFPAEGSEMVVVKGVEFYSMCEHHLLPFFGKVHIGYIPDGKILGLSKFARIVDMFARRLQVQERLAVQIAEAIQEVLEPQGVGVVVEGVHLCMMMRGVEKQHSRTVTSAMLGVFRENQKTREEFLSHLR 216
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: T-fold (116)

Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like (113)

Family: GTP cyclohydrolase I (15)

Protein domain: GTP cyclohydrolase I (14)

Thermus thermophilus [TaxId: 274] (3)

1a	d1wm9a1	A:32-216
1b	d1wm9b_	B:
1c	d1wm9c_	C:
1d	d1wm9d_	D:
1e	d1wm9e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: GTP Cyclohydrolase I, domain 2 (31)

Homologous Superfamily: [code=3.30.1130.10, no name defined] (31)

Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. (1)

1a	1wm9A02	A:86-216
1b	1wm9B02	B:86-216
1c	1wm9C02	C:86-216
1d	1wm9D02	D:86-216
1e	1wm9E02	E:86-216

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: GTP Cyclohydrolase I; Chain A, domain 1 (23)

Homologous Superfamily: [code=1.10.286.10, no name defined] (14)

Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. (1)

2a	1wm9A01	A:32-85
2b	1wm9B01	B:32-85
2c	1wm9C01	C:32-85
2d	1wm9D01	D:32-85
2e	1wm9E01	E:33-85

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: THBO-biosyn (64)

Family: GTP_cyclohydroI (9)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (3)

1a	GTP_cyclohydroI-1wm9E01	E:114-199
1b	GTP_cyclohydroI-1wm9E02	E:114-199
1c	GTP_cyclohydroI-1wm9E03	E:114-199
1d	GTP_cyclohydroI-1wm9E04	E:114-199
1e	GTP_cyclohydroI-1wm9E05	E:114-199

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (Q5SH52_THET8 | Q5SH52)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003934	GTP cyclohydrolase I activity	Catalysis of the reaction: GTP + H2O = formate + 7,8-dihydroneopterin 3'-triphosphate.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0035998	7,8-dihydroneopterin 3'-triphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of 7,8-dihydroneopterin 3'-triphosphate.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0046654	tetrahydrofolate biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(no "Related Entries Specified in the PDB File" available for 1WM9)

Description

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Ligands, Modified Residues, Ions (1, 5)

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