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Title :   CRYSTAL STRUCTURE OF PUTATIVE FORMYLTETRAHYDROFOLATE SYNTHETASE (TM1766) FROM THERMOTOGA MARITIMA AT 1.85 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   03 Jul 08 (Deposition) - 02 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Tm1766, Putative Formyltetrahydrofolate Synthetase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Atp-Binding, Ligase, Nucleotide-Binding, One-Carbon Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Formyltetrahydrofolate Synthetase (Tm1766) From Thermotoga Maritima At 1. 85 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - FORMATE--TETRAHYDROFOLATE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MH1
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FHS, TM_1766
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	FORMYLTETRAHYDROFOLATE SYNTHETASE, FHS, FTHFS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 45)

No.	Name	Count	Type	Full Name
1	EDO	19	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	26	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 90)

No.	Name	Count	Type	Full Name
1	EDO	38	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	52	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:1030 , ILE B:136 , ASN B:140 , HOH B:586 , HOH B:844	BINDING SITE FOR RESIDUE EDO B 543
02	AC2	SOFTWARE	ASP A:145 , THR A:147 , ARG A:148 , LYS B:137 , SER B:172 , PHE B:176	BINDING SITE FOR RESIDUE EDO B 544
03	AC3	SOFTWARE	ARG A:148 , LYS B:137 , SER B:172 , ALA B:173 , HOH B:782	BINDING SITE FOR RESIDUE EDO B 545
04	AC4	SOFTWARE	PHE A:500 , HOH A:1027	BINDING SITE FOR RESIDUE EDO A 543
05	AC5	SOFTWARE	LEU A:499	BINDING SITE FOR RESIDUE EDO A 544
06	AC6	SOFTWARE	ARG B:82 , PHE B:260 , ALA B:261 , GLY B:288 , PHE B:289	BINDING SITE FOR RESIDUE EDO B 546
07	AC7	SOFTWARE	ILE A:136 , ASN A:140 , PHE A:176 , HOH A:663 , HOH A:888 , HOH A:1030	BINDING SITE FOR RESIDUE EDO A 545
08	AC8	SOFTWARE	LYS A:137 , SER A:172 , PHE A:176 , ASP B:145 , THR B:147 , ARG B:148	BINDING SITE FOR RESIDUE EDO A 546
09	AC9	SOFTWARE	HIS A:135 , LEU A:226 , HOH A:845 , HOH B:871	BINDING SITE FOR RESIDUE EDO A 547
10	BC1	SOFTWARE	HIS B:135 , ASP B:225 , LEU B:226	BINDING SITE FOR RESIDUE EDO B 547
11	BC2	SOFTWARE	PHE B:150 , PHE B:500 , HOH B:839	BINDING SITE FOR RESIDUE EDO B 549
12	BC3	SOFTWARE	LEU A:11 , GLU A:12	BINDING SITE FOR RESIDUE EDO A 548
13	BC4	SOFTWARE	GLY A:170 , SER B:164 , GLU B:179	BINDING SITE FOR RESIDUE EDO B 550
14	BC5	SOFTWARE	ARG A:349 , LEU A:387 , LEU B:423 , HOH B:886 , HOH B:925	BINDING SITE FOR RESIDUE EDO B 551
15	BC6	SOFTWARE	GLU A:109 , TYR B:21 , HOH B:835 , HOH B:883	BINDING SITE FOR RESIDUE EDO B 552
16	BC7	SOFTWARE	TYR A:21 , ASP A:238 , HOH A:899 , TYR B:21 , GLY B:22 , GLU B:109	BINDING SITE FOR RESIDUE EDO A 549
17	BC8	SOFTWARE	ASN B:529 , HOH B:759	BINDING SITE FOR RESIDUE EDO B 553
18	BC9	SOFTWARE	ASP B:41 , GLY B:42 , ASP B:417	BINDING SITE FOR RESIDUE EDO B 554

(no "SS Bond" information available for 3DO6)

Asymmetric Unit

No.	Residues
1	Leu A:105	-	Pro A:106
2	Leu B:105	-	Pro B:106

(no "SAP(SNP)/Variant" information available for 3DO6)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FTHFS_1	PS00721	Formate--tetrahydrofolate ligase signature 1.	FTHS_THEMA	91-101	2	A:91-101 B:91-101
2	FTHFS_2	PS00722	Formate--tetrahydrofolate ligase signature 2.	FTHS_THEMA	316-327	2	A:316-327 B:316-327

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FTHFS_1	PS00721	Formate--tetrahydrofolate ligase signature 1.	FTHS_THEMA	91-101	4	A:91-101 B:91-101
2	FTHFS_2	PS00722	Formate--tetrahydrofolate ligase signature 2.	FTHS_THEMA	316-327	4	A:316-327 B:316-327

(no "Exon" information available for 3DO6)

Asymmetric Unit

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	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:543
 aligned with FTHS_THEMA | Q9X287 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:543
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539   
           FTHS_THEMA     - -MKPIKEIADQLELKDDILYPYGHYIAKIDHRFLKSLENHEDGKLILVTAVTPTPAGEGKTTTSIGLSMSLNRIGKKSIVTLREPSLGPTLGLKGGATGGGRSRVLPSDEINLHFTGDMHAVASAHNLLAAVLDSHIKHGNELKIDITRVFWKRTMDMNDRALRSIVIGLGGSANGFPREDSFIITAASEVMAILALSENMKDLKERLGKIIVALDADRKIVRISDLGIQGAMAVLLKDAINPNLVQTTEGTPALIHCGPFANIAHGTNSIIATKMAMKLSEYTVTEAGFGADLGAEKFIDFVSRVGGFYPNAAVLVATVRALKYHGGANLKNIHEENLEALKEGFKNLRVHVENLRKFNLPVVVALNRFSTDTEKEIAYVVKECEKLGVRVAVSEVFKKGSEGGVELAKAVAEAAKDVEPAYLYEMNDPVEKKIEILAKEIYRAGRVEFSDTAKNALKFIKKHGFDELPVIVAKTPKSISHDPSLRGAPEGYTFVVSDLFVSAGAGFVVALSGDINLMPGLPKKPNALNMDVDDSGNIVGVS 542
               SCOP domains d3do6a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3do6A01 A:0-116,A:236-428 P-loop containing nucleotide triphosphate hydrolases                                       3do6A02 A:117-235 Domain 2, N(10)-formyltetrahydrofolate synthetase                                                    3do6A01 A:0-116,A:236-428 P-loop containing nucleotide triphosphate hydrolases                                                                                                                   ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..hhh.eeee...eeee..hhhhhh......eeeeeee........hhhhhhhhhhhhhhhh...eeeee...hhhhhhhh.....ee..eeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...eee...hhhhh.eee...hhhhh..eee.eee...hhhhhhhhhh.hhhhhhhhhhh.eeeee....eeehhhhhhhhhhhhhh......eeeee....eeee.............hhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhh......eeee...................eeee.eeeee....eeeee.............hhhhhhee.....ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------FTHFS_1    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FTHFS_2     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3do6 A   0 GmKPIKEIADQLELKDDILYPYGHYIAKIDHRFLKSLENHEDGKLILVTAVTPTPAGEGKTTTSIGLSmSLNRIGKKSIVTLREPSLGPTLGLKGGATGGGRSRVLPSDEINLHFTGDmHAVASAHNLLAAVLDSHIKHGNELKIDITRVFWKRTmDmNDRALRSIVIGLGGSANGFPREDSFIITAASEVmAILALSENmKDLKERLGKIIVALDADRKIVRISDLGIQGAmAVLLKDAINPNLVQTTEGTPALIHCGPFANIAHGTNSIIATKmAmKLSEYTVTEAGFGADLGAEKFIDFVSRVGGFYPNAAVLVATVRALKYHGGANLKNIHEENLEALKEGFKNLRVHVENLRKFNLPVVVALNRFSTDTEKEIAYVVKECEKLGVRVAVSEVFKKGSEGGVELAKAVAEAAKDVEPAYLYEmNDPVEKKIEILAKEIYRAGRVEFSDTAKNALKFIKKHGFDELPVIVAKTPKSISHDPSLRGAPEGYTFVVSDLFVSAGAGFVVALSGDINLmPGLPKKPNALNmDVDDSGNIVGVS 542
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     | 159       169       179       189 |     199|      209       219       229  |    239       249       259       269     | 279       289       299       309       319       329       339       349       359       369       379       389       399       409       419      |429       439       449       459       469       479       489       499       509       519       529|      539   
                             |                                                                 68-MSE                                           118-MSE                              155-MSE                             191-MSE  200-MSE                         232-MSE                                    275-MSE                                                                                                                                                426-MSE                                                                                     518-MSE     530-MSE        
                             1-MSE                                                                                                                                                     157-MSE                                                                                                                 277-MSE

Chain B from PDB  Type:PROTEIN  Length:543
 aligned with FTHS_THEMA | Q9X287 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:543
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539   
           FTHS_THEMA     - -MKPIKEIADQLELKDDILYPYGHYIAKIDHRFLKSLENHEDGKLILVTAVTPTPAGEGKTTTSIGLSMSLNRIGKKSIVTLREPSLGPTLGLKGGATGGGRSRVLPSDEINLHFTGDMHAVASAHNLLAAVLDSHIKHGNELKIDITRVFWKRTMDMNDRALRSIVIGLGGSANGFPREDSFIITAASEVMAILALSENMKDLKERLGKIIVALDADRKIVRISDLGIQGAMAVLLKDAINPNLVQTTEGTPALIHCGPFANIAHGTNSIIATKMAMKLSEYTVTEAGFGADLGAEKFIDFVSRVGGFYPNAAVLVATVRALKYHGGANLKNIHEENLEALKEGFKNLRVHVENLRKFNLPVVVALNRFSTDTEKEIAYVVKECEKLGVRVAVSEVFKKGSEGGVELAKAVAEAAKDVEPAYLYEMNDPVEKKIEILAKEIYRAGRVEFSDTAKNALKFIKKHGFDELPVIVAKTPKSISHDPSLRGAPEGYTFVVSDLFVSAGAGFVVALSGDINLMPGLPKKPNALNMDVDDSGNIVGVS 542
               SCOP domains d3do6b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3do6B01 B:0-116,B:236-428 P-loop containing nucleotide triphosphate hydrolases                                       3do6B02 B:117-235 Domain 2, N(10)-formyltetrahydrofolate synthetase                                                    3do6B01 B:0-116,B:236-428 P-loop containing nucleotide triphosphate hydrolases                                                                                                                   ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..hhh.eee.....eee..hhhhhh......eeeeeee........hhhhhhhhhhhhhhhh...eeeee...hhhhhhhh.....ee..eeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...eee...hhhhh.eee...hhhhh..eee.eee...hhhhhhhhhh.hhhhhhhhhhhheeeee....eeehhhhhhhhhhhhhh......eeeee....eeee.............hhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhh......eeee...................eeee.eeeee....eeeee.............hhhhhheee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------FTHFS_1    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FTHFS_2     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3do6 B   0 GmKPIKEIADQLELKDDILYPYGHYIAKIDHRFLKSLENHEDGKLILVTAVTPTPAGEGKTTTSIGLSmSLNRIGKKSIVTLREPSLGPTLGLKGGATGGGRSRVLPSDEINLHFTGDmHAVASAHNLLAAVLDSHIKHGNELKIDITRVFWKRTmDmNDRALRSIVIGLGGSANGFPREDSFIITAASEVmAILALSENmKDLKERLGKIIVALDADRKIVRISDLGIQGAmAVLLKDAINPNLVQTTEGTPALIHCGPFANIAHGTNSIIATKmAmKLSEYTVTEAGFGADLGAEKFIDFVSRVGGFYPNAAVLVATVRALKYHGGANLKNIHEENLEALKEGFKNLRVHVENLRKFNLPVVVALNRFSTDTEKEIAYVVKECEKLGVRVAVSEVFKKGSEGGVELAKAVAEAAKDVEPAYLYEmNDPVEKKIEILAKEIYRAGRVEFSDTAKNALKFIKKHGFDELPVIVAKTPKSISHDPSLRGAPEGYTFVVSDLFVSAGAGFVVALSGDINLmPGLPKKPNALNmDVDDSGNIVGVS 542
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149     | 159       169       179       189 |     199|      209       219       229  |    239       249       259       269     | 279       289       299       309       319       329       339       349       359       369       379       389       399       409       419      |429       439       449       459       469       479       489       499       509       519       529|      539   
                             1-MSE                                                             68-MSE                                           118-MSE                              155-MSE                             191-MSE  200-MSE                         232-MSE                                    275-MSE                                                                                                                                                426-MSE                                                                                     518-MSE     530-MSE        
                                                                                                                                                                                       157-MSE                                                                                                                 277-MSE

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) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: automated matches (303)

Protein domain: automated matches (303)

Thermotoga maritima [TaxId: 2336] (7)

1a	d3do6a_	A:
1b	d3do6b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Domain 2, N(10)-formyltetrahydrofolate synthetase (4)

Homologous Superfamily: Domain 2, N(10)-formyltetrahydrofolate synthetase (4)

Thermotoga maritima. Organism_taxid: 2336. (1)

1a	3do6A02	A:117-235
1b	3do6B02	B:117-235

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Thermotoga maritima. Organism_taxid: 2336. (16)

2a	3do6A01	A:0-116,A:236-428
2b	3do6B01	B:0-116,B:236-428

(no "Pfam Domain" information available for 3DO6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FTHS_THEMA | Q9X287)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004329	formate-tetrahydrofolate ligase activity	Catalysis of the reaction: ATP + formate + tetrahydrofolate = ADP + phosphate + 10-formyltetrahydrofolate.
	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.
biological process
	GO:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0035999	tetrahydrofolate interconversion	The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 45)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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