1KQ4 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF A THY1-COMPLEMENTING PROTEIN (TM0449) FROM THERMOTOGA MARITIMA AT 2.25 A RESOLUTION

Authors :   I. A. Wilson, M. D. Miller, Joint Center For Structural Genomics (

Date :   03 Jan 02 (Deposition) - 27 Feb 02 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Thy1-Complementing Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. A. Lesley, P. Kuhn, A. Godzik, A. M. Deacon, I. Mathews, A. Kreusch, G. Spraggon, H. E. Klock, D. Mcmullan, T. Shin, J. Vincent, A. Robb, L. S. Brinen, M. D. Miller, T. M. Mcphillips, M. A. Miller, D. Scheibe, J. M. Canaves, C. Guda, L. Jaroszewski, T. L. Selby, M. -A. Elsliger, J. Wooley, S. S. Taylor, K. O. Hodgson, I. A. Wilson, P. G. Schultz, R. C. Stevens
Structural Genomics Of The Thermotoga Maritima Proteome Implemented In A High-Throughput Structure Determination Pipeline
Proc. Natl. Acad. Sci. Usa V. 99 11664 2002
PubMed-ID: 12193646 | Reference-DOI: 10.1073/PNAS.142413399

Molecule 1 - HYPOTHETICAL PROTEIN TM0449
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMH1
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0449
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 20)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:85 , GLU A:86 , SER A:88 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , FAD B:310 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , ARG D:174 , HIS D:178 , HOH D:342 , HOH D:361 , HOH D:363 , HOH D:491	BINDING SITE FOR RESIDUE FAD D 300
2	AC2	SOFTWARE	THR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FAD A:315 , ASN B:85 , GLU B:86 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , ARG C:174 , HIS C:178 , HOH C:322 , HOH C:340 , HOH C:356 , HOH C:377 , HOH C:517 , HOH C:518 , HOH C:581	BINDING SITE FOR RESIDUE FAD C 305
3	AC3	SOFTWARE	ARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169 , LEU B:173 , ARG B:174 , HIS B:178 , HOH B:337 , HOH B:364 , HOH B:441 , SER C:83 , ASN C:85 , GLU C:86 , SER C:88 , ARG C:90 , THR D:55 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FAD D:300	BINDING SITE FOR RESIDUE FAD B 310
4	AC4	SOFTWARE	ARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , ARG A:174 , HIS A:178 , HOH A:332 , HOH A:495 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FAD C:305 , SER D:83 , ASN D:85 , GLU D:86 , SER D:88	BINDING SITE FOR RESIDUE FAD A 315

(no "SS Bond" information available for 1KQ4)

(no "Cis Peptide Bond" information available for 1KQ4)

(no "SAP(SNP)/Variant" information available for 1KQ4)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYX	PS51331	Flavin-dependent thymidylate synthase (thyX) domain profile.	THYX_THEMA	1-208	4	A:1-208 B:1-208 C:1-208 D:1-208

(no "Exon" information available for 1KQ4)

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:203
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:216
                             1                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      
           THYX_THEMA     - -MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
               SCOP domains d1kq4a_ A: Thy1 homologue                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhh..-------hhhhhhhhhhhhhh.hhhhhh.eeeeeeeeehhhhhhhh.....eeee..------.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -THYX  PDB: A:1-208 UniProt: 1-208                                                                                                                                                                               ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kq4 A   0 HmKIDILDKGFVELVDVmGNDLSAVRAARVSF-------ERDRHLIEYLmKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELS------SYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLmNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                             |       9       |19        29 |      39        49        59        69        79        |-     |  99       109       119       129       139       149       159       169       179       189       199       209      
                             |              17-MSE        31      39        49-MSE                                 88     95                                                                      168-MSE                                           
                             1-MSE

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           THYX_THEMA     1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
               SCOP domains d1kq4b_ B: Thy1 homologue                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..------hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee......---......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: B:1-208 UniProt: 1-208                                                                                                                                                                               ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kq4 B   1 mKIDILDKGFVELVDVmGNDLSAVRAARVSF------EERDRHLIEYLmKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYS---YEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLmNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                            |       10      | 20        30|      |40        50        60        70        80        90 |   | 100       110       120       130       140       150       160       170       180       190       200       210       220
                            1-MSE          17-MSE        31     38         49-MSE                                     92  96                                                                     168-MSE

Chain C from PDB  Type:PROTEIN  Length:214
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           THYX_THEMA     1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
               SCOP domains d1kq4c_ C: Thy1 homologue                                                                                                                                                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh...----hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee.....--........hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: C:1-208 UniProt: 1-208                                                                                                                                                                               ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kq4 C   1 mKIDILDKGFVELVDVmGNDLSAVRAARVSFD----DEERDRHLIEYLmKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRY--LSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLmNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV 220
                            |       10      | 20        30 |    | 40        50        60        70        80        90|  |   100       110       120       130       140       150       160       170       180       190       200       210       220
                            1-MSE          17-MSE         32   37          49-MSE                                    91 94                                                                       168-MSE

Chain D from PDB  Type:PROTEIN  Length:210
 aligned with THYX_THEMA | Q9WYT0 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
           THYX_THEMA     1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
               SCOP domains d1kq4d_ D: Thy1 homologue                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Thy1-1kq4D01 D:11-201                                                                                                                                                                          -------------- Pfam domains (1)
           Pfam domains (2) ----------Thy1-1kq4D02 D:11-201                                                                                                                                                                          -------------- Pfam domains (2)
           Pfam domains (3) ----------Thy1-1kq4D03 D:11-201                                                                                                                                                                          -------------- Pfam domains (3)
           Pfam domains (4) ----------Thy1-1kq4D04 D:11-201                                                                                                                                                                          -------------- Pfam domains (4)
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..-----hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: D:1-208 UniProt: 1-208                                                                                                                                                                               ------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kq4 D   1 mKIDILDKGFVELVDVmGNDLSAVRAARVSF-----DEERDRHLIEYLmKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLmNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                            |       10      | 20        30|     | 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                            1-MSE          17-MSE        31    37          49-MSE                                                                                                                168-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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Thymidylate synthase-complementing protein Thy1 (24)

Superfamily: Thymidylate synthase-complementing protein Thy1 (24)

Family: Thymidylate synthase-complementing protein Thy1 (24)

Protein domain: Thy1 homologue (22)

Thermotoga maritima [TaxId: 2336] (22)

1a	d1kq4a_	A:
1b	d1kq4b_	B:
1c	d1kq4c_	C:
1d	d1kq4d_	D:

(no "CATH Domain" information available for 1KQ4)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Thy1] (11)

Family: Thy1 (11)

Thermotoga maritima (11)

1a	Thy1-1kq4D01	D:11-201
1b	Thy1-1kq4D02	D:11-201
1c	Thy1-1kq4D03	D:11-201
1d	Thy1-1kq4D04	D:11-201

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (THYX_THEMA | Q9WYT0)

molecular function
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0050797	thymidylate synthase (FAD) activity	Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP + NADPH + H+ = dTMP + tetrahydrofolate + NADP+.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006231	dTMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).

Asymmetric/Biological Unit
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1kq3	CRYSTAL STRUCTURE OF GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION RELATED ID: 282322 RELATED DB: TARGETDB

Description

Compounds

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Ligands, Modified Residues, Ions (2, 20)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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