1VK3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II (TM1246) FROM THERMOTOGA MARITIMA AT 2.15 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   23 Apr 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym./Biol. Unit : A

Keywords :   Tm1246, Phosphoribosylformylglycinamidine Synthase Ii, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. I. Mathews, S. S. Krishna, R. Schwarzenbacher, D. Mcmullan, P. Abdubek, E. Ambing, J. M. Canaves, H. J. Chiu, A. M. Deacon, M. Didonato, M. A. Elsliger, A. Godzik, C. Grittini, S. K. Grzechnik, J. Hale, E. Hampton, G. W. Han, J. Haugen, L. Jaroszewski, H. E. Klock, E. Koesema, A. Kreusch, P. Kuhn, S. A. Lesley, I. Levin, M. D. Miller, K. Moy, E. Nigoghossian, J. Paulsen, K. Quijano, R. Reyes, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of Phosphoribosylformylglycinamidine Synthase Ii (Smpurl) From Thermotoga Maritima At 2. 15 A Resolution.
Proteins V. 63 1106 2006
PubMed-ID: 16544324 | Reference-DOI: 10.1002/PROT.20650
(for further references see the PDB file header)

Molecule 1 - PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE II
	Chains	:	A
	EC Number	:	6.3.5.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PURL, TM1246
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	FGAM SYNTHASE II

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 17)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1VK3)

(no "SS Bond" information available for 1VK3)

(no "Cis Peptide Bond" information available for 1VK3)

(no "SAP(SNP)/Variant" information available for 1VK3)

(no "PROSITE Motif" information available for 1VK3)

(no "Exon" information available for 1VK3)

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
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Chain A from PDB  Type:PROTEIN  Length:586
 aligned with PURL_THEMA | Q9X0X3 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:602
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601  
           PURL_THEMA     2 KLRYLNILKEKLGREPTFVELQAFSVMWSEHCGYSHTKKYIRRLPKTGFEGNAGVVNLDDYYSVAFKIESHNHPSAIEPYNGAATGVGGIIRDVLAMGARPTAIFDSLHMSRIIDGIIEGIADYGNSIGVPTVGGELRISSLYAHNPLVNVLAAGVVRNDMLVDSKASRPGQVIVIFGGATGRDGIHGASFASEDLTGDKATKLSIQVGDPFAEKMLIEAFLEMVEEGLVEGAQDLGAGGVLSATSELVAKGNLGAIVHLDRVPLREPDMEPWEILISESQERMAVVTSPQKASRILEIARKHLLFGDVVAEVIEEPVYRVMYRNDLVMEVPVQLLANAPEEDIVEYTPGKIPEFKRVEFEEVNAREVFEQYDHMVGTDTVVPPGFGAAVMRIKRDGGYSLVTHSRADLALQDTYWGTLIAVLESVRKTLSVGAEPLAITNCVNYGDPDVDPVGLSAMMTALKNACEFSGVPVASGNASLYNTYQGKPIPPTLVVGMLGKVNPQKVAKPKPSKVFAVGWNDFELEREKELWRAIRKLSEEGAFILSSSQLLTRTHVETFREYGLKIEVKLPEVRPAHQMVLVFSERTPVVDVPVKEIGTLSR 603
               SCOP domains d1vk3a1 A:2-166 Phosphoribosylformylglycinamidine synthase II, domains 1 and 3                                                                                       d1vk3a3 A:167-345 Ph                osphoribosylformylglycinamidine synthase II, domains 2 and 4                                                                                   d1vk3a2 A:346-507 Phosphoribosylformylglycinamidine synthase II, domains 1 and 3                                                                                  d1vk3a4 A:508-603 Phosphoribosylformylglycinamidine synthase II, domains 2 and 4                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-1vk3A03 A:                170-325                                                                                                                    ------------------------------------------------------------AIRS-1vk3A01 A:386-479                                                                        ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS-1vk3A02 A:386-479                                                                        ---------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhh...........eee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhh...eeeeeeee.hhhh...eeeeeeeeeee..............eeeeee.......----------------hhhhh....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeee.hhh.......hhhhhhhh....eeeeeehhh.hhhhhhhhhhh..eeeeeeeee...eeeeee..eeeeeeehhhhhh......................ee.hhhhhhh............hhhhh.eeeeee..eeeeeeee.hhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeeee...ee..ee...eeeeeeeeeehhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh..eeee.........eeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk3 A   2 KLRYLNILKEKLGREPTFVELQAFSVmWSEHCGYSHTKKYIRRLPKTGFEGNAGVVNLDDYYSVAFKIESHNHPSAIEPYNGAATGVGGIIRDVLAmGARPTAIFDSLHmSRIIDGIIEGIADYGNSIGVPTVGGELRISSLYAHNPLVNVLAAGVVRNDmLVDSKASRPGQVIVIFGGATGRDG----------------TKLSIQVGDPFAEKmLIEAFLEmVEEGLVEGAQDLGAGGVLSATSELVAKGNLGAIVHLDRVPLREPDmEPWEILISESQERmAVVTSPQKASRILEIARKHLLFGDVVAEVIEEPVYRVmYRNDLVmEVPVQLLANAPEEDIVEYTPGKIPEFKRVEFEEVNAREVFEQYDHmVGTDTVVPPGFGAAVmRIKRDGGYSLVTHSRADLALQDTYWGTLIAVLESVRKTLSVGAEPLAITNCVNYGDPDVDPVGLSAmmTALKNACEFSGVPVASGNASLYNTYQGKPIPPTLVVGmLGKVNPQKVAKPKPSKVFAVGWNDFELEREKELWRAIRKLSEEGAFILSSSQLLTRTHVETFREYGLKIEVKLPEVRPAHQmVLVFSERTPVVDVPVKEIGTLSR 603
                                    11        21      | 31        41        51        61        71        81        91      |101       111       121       131       141       151       161|      171       181    |    -         - |     211     | 221   |   231       241       251       261       271       281   |   291       301       311       321 |     331       341       351       361       371    |  381       391|      401       411       421       431       441       451       461       471       481       491      |501       511       521       531       541       551       561       571       581       591       601  
                                                     28-MSE                                                                98-MSE      111-MSE                                            162-MSE                 186              203           217-MSE 225-MSE                                       271-MSE       285-MSE                               323-MSE  |                                           376-MSE         392-MSE                                                            459-MSE                                498-MSE                                                                           580-MSE                   
                                                                                                                                                                                                                                                                                                                                                                  330-MSE                                                                                                                           460-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "CATH Domain" information available for 1VK3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: AIRS] (11)

Family: AIRS (11)

Thermotoga maritima (1)

1a	AIRS-1vk3A01	A:386-479
1b	AIRS-1vk3A02	A:386-479

Clan: no clan defined [family: AIRS_C] (13)

Family: AIRS_C (13)

Thermotoga maritima (1)

AIRS_C-1vk3A03

A:170-325

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PURL_THEMA | Q9X0X3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0004642	phosphoribosylformylglycinamidine synthase activity	Catalysis of the reaction: N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + ATP + H(2)O = 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate + ADP + 2 H(+) + phosphate.
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:0006541	glutamine metabolic process	The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
	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.
	GO:0009156	ribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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