1VK8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   05 May 04 (Deposition) - 18 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Protein With Possible Role In Cell Wall Biogenesis, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Dermoun, A. Foulon, M. D. Miller, D. J. Harrington, A. M. Deacon, C. Sebban-Kreuzer, P. Roche, D. Lafitte, O. Bornet, I. A. Wilson, A. Dolla
Tm0486 From The Hyperthermophilic Anaerobe Thermotoga Maritima Is A Thiamin-Binding Protein Involved In Response Of The Cell To Oxidative Conditions.
J. Mol. Biol. V. 400 463 2010
PubMed-ID: 20471400 | Reference-DOI: 10.1016/J.JMB.2010.05.014

Molecule 1 - HYPOTHETICAL PROTEIN TM0486
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0486
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Other Details	:	PROTEIN WITH POSSIBLE ROLE IN CELL WALL BIOGENESIS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	UNL	4	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:8 , LYS A:9 , VAL A:10 , HIS A:20 , ILE A:23 , VAL A:39 , GLY A:40 , PRO A:41 , SER A:42 , ASN A:43 , THR A:44 , HOH A:477	BINDING SITE FOR RESIDUE UNL A 400
2	AC2	SOFTWARE	ILE B:8 , LYS B:9 , VAL B:10 , HIS B:20 , VAL B:39 , GLY B:40 , PRO B:41 , SER B:42 , ASN B:43 , THR B:44 , LYS D:89	BINDING SITE FOR RESIDUE UNL B 400
3	AC3	SOFTWARE	LYS A:89 , ILE C:8 , LYS C:9 , VAL C:10 , ILE C:23 , ILE C:30 , VAL C:39 , GLY C:40 , PRO C:41 , ASN C:43 , THR C:44	BINDING SITE FOR RESIDUE UNL C 400
4	AC4	SOFTWARE	LYS B:89 , ILE D:8 , LYS D:9 , VAL D:10 , ILE D:30 , VAL D:39 , GLY D:40 , PRO D:41 , SER D:42 , ASN D:43 , THR D:44	BINDING SITE FOR RESIDUE UNL D 400

(no "SS Bond" information available for 1VK8)

(no "Cis Peptide Bond" information available for 1VK8)

(no "SAP(SNP)/Variant" information available for 1VK8)

(no "PROSITE Motif" information available for 1VK8)

(no "Exon" information available for 1VK8)

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:93
 aligned with Q9WYV6_THEMA | Q9WYV6 from UniProtKB/TrEMBL  Length:94

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
          Q9WYV6_THEMA    2 PKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGMKYEVGPSNTTVEGEFEEIMDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
               SCOP domains d1vk8a_ A: Hypothetical protein TM0486                                                        SCOP domains
               CATH domains 1vk8A00 A:2-94  [code=3.30.70.930, no name defined]                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhh....eee....eeeeehhhhhhhhhhhhhhhhh....eeeeeeeeeee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  1vk8 A  2 PKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGmKYEVGPSNTTVEGEFEEImDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
                                    11        21        31   |    41        51  |     61        71        81        91   
                                                            35-MSE             54-MSE

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with Q9WYV6_THEMA | Q9WYV6 from UniProtKB/TrEMBL  Length:94

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
          Q9WYV6_THEMA    2 PKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGMKYEVGPSNTTVEGEFEEIMDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
               SCOP domains d1vk8b_ B: Hypothetical protein TM0486                                                        SCOP domains
               CATH domains 1vk8B00 B:2-94  [code=3.30.70.930, no name defined]                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhhhhhhhhhh....eee....eeeeeehhhhhhhhhhhhhhhh....eeeeeeeeeee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  1vk8 B  2 PKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGmKYEVGPSNTTVEGEFEEImDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
                                    11        21        31   |    41        51  |     61        71        81        91   
                                                            35-MSE             54-MSE

Chain C from PDB  Type:PROTEIN  Length:94
 aligned with Q9WYV6_THEMA | Q9WYV6 from UniProtKB/TrEMBL  Length:94

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
          Q9WYV6_THEMA    1 MPKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGMKYEVGPSNTTVEGEFEEIMDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
               SCOP domains d1vk8c_ C: Hypothetical protein TM0486                                                         SCOP domains
               CATH domains -1vk8C00 C:2-94  [code=3.30.70.930, no name defined]                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..hhhhhhhhhhhhhhhhhh...eeee....eeeeehhhhhhhhhhhhhhhhh....eeeeeeeeeee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  1vk8 C  1 mPKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGmKYEVGPSNTTVEGEFEEImDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
                            |       10        20        30    |   40        50   |    60        70        80        90    
                            1-MSE                            35-MSE             54-MSE

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with Q9WYV6_THEMA | Q9WYV6 from UniProtKB/TrEMBL  Length:94

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
          Q9WYV6_THEMA    2 PKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGMKYEVGPSNTTVEGEFEEIMDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
               SCOP domains d1vk8d_ D: Hypothetical protein TM0486                                                        SCOP domains
               CATH domains 1vk8D00 D:2-94  [code=3.30.70.930, no name defined]                                           CATH domains
           Pfam domains (1) ----DUF77-1vk8D01 D:6-94                                                                      Pfam domains (1)
           Pfam domains (2) ----DUF77-1vk8D02 D:6-94                                                                      Pfam domains (2)
           Pfam domains (3) ----DUF77-1vk8D03 D:6-94                                                                      Pfam domains (3)
           Pfam domains (4) ----DUF77-1vk8D04 D:6-94                                                                      Pfam domains (4)
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhh....eee....eeeeehhhhhhhhhhhhhhhhh....eeeeeeeeeee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  1vk8 D  2 PKVTVSIKVVPAVEDGRLHEVIDRAIEKISSWGmKYEVGPSNTTVEGEFEEImDRVKELARYLEQFAKRFVLQLDIDYKAGGITIEEKVSKYR 94
                                    11        21        31   |    41        51  |     61        71        81        91   
                                                            35-MSE             54-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: Ferredoxin-like (1795)

Superfamily: MTH1187/YkoF-like (11)

Family: MTH1187-like (5)

Protein domain: Hypothetical protein TM0486 (1)

Thermotoga maritima [TaxId: 2336] (1)

1a	d1vk8a_	A:
1b	d1vk8b_	B:
1c	d1vk8c_	C:
1d	d1vk8d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.930, no name defined] (10)

Thermotoga maritima. Organism_taxid: 2336. (1)

1a	1vk8A00	A:2-94
1b	1vk8B00	B:2-94
1c	1vk8C00	C:2-94
1d	1vk8D00	D:2-94

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MTH1187-YkoF (6)

Family: DUF77 (4)

Thermotoga maritima (1)

1a	DUF77-1vk8D01	D:6-94
1b	DUF77-1vk8D02	D:6-94
1c	DUF77-1vk8D03	D:6-94
1d	DUF77-1vk8D04	D:6-94

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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