2DPL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE GMP SYNTHASE FROM PYROCOCCUS HORIKOSHII OT3

Authors :   Y. Asada, N. Kunishima, Riken Structural Genomics/Proteomics Ini (Rsgi)

Date :   12 May 06 (Deposition) - 12 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.43

Chains :   Asym./Biol. Unit : A,B

Keywords :   Pyrococcus Horikoshii Ot3, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Asada, N. Kunishima
Crystal Structure Of The Gmp Synthase From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

Molecule 1 - GMP SYNTHASE [GLUTAMINE-HYDROLYZING] SUBUNIT B
	Chains	:	A, B
	EC Number	:	6.3.5.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GUAAB
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	GMP SYNTHETASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DPL)

(no "Site" information available for 2DPL)

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:300	-	Pro A:301
2	Pro A:301	-	Pro A:302
3	Lys B:300	-	Pro B:301
4	Pro B:301	-	Pro B:302

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMPS_ATP_PPASE	PS51553	GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile.	GUAAB_PYRHO	1-185	1	A:1-185

(no "Exon" information available for 2DPL)

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:287
 aligned with GUAAB_PYRHO | O59072 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:308
                                    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       260       270       280       290       300        
          GUAAB_PYRHO     1 MDWGRFVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAPDWIESQGKIKSHHNVGGLPEKLNLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
               SCOP domains d2dpla1 A:1-189 automated matches                                                                                                                                                            d2dpla2 A:190-308 automated matches                                                                                     SCOP domains
               CATH domains 2dplA01 A:1-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                    2dplA02 A:186-308  [code=3.30.300.10, no name defined]                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.....eeeeeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..eee......---------------------...eee......hhhhhhhhhhhh..hhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee....eeee....eeeeeeeeeeeee.......ee...hhhhhhhhhhhhhhhh..eeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GMPS_ATP_PPASE  PDB: A:1-185 UniProt: 1-185                                                                                                                                              --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpl A   1 MDWGRFVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAP---------------------LNLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|        -         -  |    160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
                                                                                                                                                            131                   153

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with GUAAB_PYRHO | O59072 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:303
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305   
          GUAAB_PYRHO     6 FVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTIAPDWIESQGKIKSHHNVGGLPEKLNLKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
               SCOP domains d2dplb1 B:6-189 automated matches                                                                                                                                                       d2dplb2 B:190-308 automated matches                                                                                     SCOP domains
               CATH domains 2dplB01 B:6-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                               2dplB02 B:186-308  [code=3.30.300.10, no name defined]                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..eee....-------------------------.eee......hhhhhhhhhhhhh.hhhhhh......hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....eeeeee................eeeeeeeeee.....eee...hhhhhhhhhhhhhhhh..eeeeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GMPS_ATP_PPASE  PDB: - UniProt: 1-185                                                                                                                                               --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpl B   6 FVEEKVREIRETVGDSKAIIALSGGVDSSTAAVLAHKAIGDRLHAVFVNTGFLRKGEPEFVVKTFRDEFGMNLHYVDAQDRFFSALKGVTDPEEKRKIIGRVFIEVFEEVAKKIGAEYLIQGTI-------------------------LKLIEPLRDLYKDEVRELAKFLGLPEKIYNRMPFPGPGLAVRVIGEVTPEKIRIVREANAIVEEEVERAGLRPWQAFAVLLGVKTVGVQGDIRAYKETIAVRIVESIDGMTANAMNVPWEVLQRIAFRITSEIPEVGRVLYDITNKPPATIEFE 308
                                    15        25        35        45        55        65        75        85        95       105       115       125   |     -         -       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305   
                                                                                                                                                     129                       155

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 '\|'

(no "Pfam Domain" information available for 2DPL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GUAAB_PYRHO | O59072)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003922	GMP synthase (glutamine-hydrolyzing) activity	Catalysis of the reaction: ATP + xanthosine 5'-phosphate + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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:0016462	pyrophosphatase activity	Catalysis of the hydrolysis of a pyrophosphate bond between two phosphate groups, leaving one phosphate on each of the two fragments.
biological process
	GO:0006177	GMP biosynthetic process	The chemical reactions and pathways resulting in the formation of GMP, guanosine 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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2dpl)

	Sites
(no "Sites" information available for 2dpl)

	Cis Peptide Bonds
		Lys A:300 - Pro A:301	[ RasMol ]
		Lys B:300 - Pro B:301	[ RasMol ]
		Pro A:301 - Pro A:302	[ RasMol ]
		Pro B:301 - Pro B:302	[ RasMol ]

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	2dpl
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	GUAAB_PYRHO \| O59072
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	6.3.5.2
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	GUAAB_PYRHO \| O59072	:	3a4i

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

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Gene Ontology (7, 7)

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