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Description

Title :   CRYSTAL STRUCTURE OF A PUTATIVE FORMYLMETHANOFURAN DEHYDROGENASE SUBUNIT E (TA1109) FROM THERMOPLASMA ACIDOPHILUM AT 1.87 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   02 May 06 (Deposition) - 13 Jun 06 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (4x)

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. L. Axelrod, D. Das, P. Abdubek, T. Astakhova, C. Bakolitsa, D. Carlton, C. Chen, H. J. Chiu, T. Clayton, M. C. Deller, L. Duan, K. Ellrott, C. L. Farr, J. Feuerhelm, J. C. Grant, A. Grzechnik, G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, P. Kozbial S. S. Krishna, A. Kumar, W. W. Lam, D. Marciano, D. Mcmullan, M. D. Miller, A. T. Morse, E. Nigoghossian, A. Nopakun, L. Okach, C. Puckett, R. Reyes, N. Sefcovic, H. J. Tien, C. B. Trame, H. Van Den Bedem, D. Weekes, T. Wooten, Q. Xu, K. O. Hodgson, J. Wooley M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structures Of Three Members Of Pfam Pf02663 (Fmde) Implicated In Microbial Methanogenesis Reveal A Conserved Alpha+Beta Core Domain And An Auxiliary C-Terminal Treble-Clef Zinc Finger.
Acta Crystallogr. , Sect. F V. 66 1335 2010
PubMed-ID: 20944230 | Reference-DOI: 10.1107/S1744309110020166

Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	10640422
	Organism Scientific	:	THERMOPLASMA ACIDOPHILUM
	Organism Taxid	:	2303

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (5, 26)

Asymmetric Unit (5, 26)

No.	Name	Count	Type	Full Name
1	ACY	8	Ligand/Ion	ACETIC ACID
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	UNL	1	Ligand/Ion	UNKNOWN LIGAND
5	ZN	5	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 42)

No.	Name	Count	Type	Full Name
1	ACY	16	Ligand/Ion	ACETIC ACID
2	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	UNL	2	Ligand/Ion	UNKNOWN LIGAND
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 84)

No.	Name	Count	Type	Full Name
1	ACY	32	Ligand/Ion	ACETIC ACID
2	EDO	24	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
4	UNL	4	Ligand/Ion	UNKNOWN LIGAND
5	ZN	-1	Ligand/Ion	ZINC ION

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:16 , HIS A:18 , CYS A:20 , CYS A:61 , UNL A:400	BINDING SITE FOR RESIDUE ZN A 300
02	AC2	SOFTWARE	CYS A:174 , CYS A:177 , CYS A:195 , ASP A:198	BINDING SITE FOR RESIDUE ZN A 301
03	AC3	SOFTWARE	HIS A:102 , GLU A:153 , ACY A:410 , HOH A:472	BINDING SITE FOR RESIDUE ZN A 302
04	AC4	SOFTWARE	GLU A:130 , GLU A:149 , ACY A:411 , HOH A:521	BINDING SITE FOR RESIDUE ZN A 303
05	AC5	SOFTWARE	ASP A:117 , GLU A:156 , EDO A:406 , HOH A:513	BINDING SITE FOR RESIDUE ZN A 304
06	AC6	SOFTWARE	TYR A:22 , HIS A:45 , ASN A:59 , CYS A:61 , ARG A:122 , PRO A:128 , ZN A:300	BINDING SITE FOR RESIDUE UNL A 400
07	AC7	SOFTWARE	ASP A:117 , ARG A:120 , TYR A:121 , TYR A:154 , GLU A:156 , HOH A:463	BINDING SITE FOR RESIDUE EDO A 401
08	AC8	SOFTWARE	HOH A:456	BINDING SITE FOR RESIDUE EDO A 402
09	AC9	SOFTWARE	ASN A:63 , TYR A:74 , GLY A:75	BINDING SITE FOR RESIDUE EDO A 403
10	BC1	SOFTWARE	LYS A:35 , ILE A:36 , ARG A:120 , LYS A:123 , GLN A:124	BINDING SITE FOR RESIDUE EDO A 404
11	BC2	SOFTWARE	ILE A:36 , ALA A:37 , ARG A:120 , GLU A:156 , EDO A:406 , HOH A:515	BINDING SITE FOR RESIDUE EDO A 405
12	BC3	SOFTWARE	ASP A:117 , GLU A:156 , ZN A:304 , EDO A:405 , HOH A:516	BINDING SITE FOR RESIDUE EDO A 406
13	BC4	SOFTWARE	ARG A:104 , ASN A:105 , SER A:106 , GLU A:153 , ACY A:410 , HOH A:475	BINDING SITE FOR RESIDUE ACY A 407
14	BC5	SOFTWARE	ASP A:175 , LYS A:192	BINDING SITE FOR RESIDUE ACY A 408
15	BC6	SOFTWARE	ARG A:100 , ARG A:155	BINDING SITE FOR RESIDUE ACY A 409
16	BC7	SOFTWARE	HIS A:102 , ASN A:105 , GLU A:153 , GLU A:179 , ZN A:302 , ACY A:407 , HOH A:472	BINDING SITE FOR RESIDUE ACY A 410
17	BC8	SOFTWARE	ARG A:104 , GLU A:130 , GLU A:149 , ZN A:303 , HOH A:521	BINDING SITE FOR RESIDUE ACY A 411
18	BC9	SOFTWARE	LYS A:86 , CYS A:177 , GLU A:179 , ASP A:198	BINDING SITE FOR RESIDUE ACY A 412
19	CC1	SOFTWARE	ARG A:28 , ASP A:148 , HOH A:423	BINDING SITE FOR RESIDUE ACY A 413
20	CC2	SOFTWARE	ASN A:5 , GLU A:10 , HOH A:538	BINDING SITE FOR RESIDUE ACY A 414

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2GVI)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2GVI)

Exons (0, 0)

(no "Exon" information available for 2GVI)

Sequences/Alignments

Asymmetric 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:201
 aligned with Q9HJ63_THEAC | Q9HJ63 from UniProtKB/TrEMBL  Length:203

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
         Q9HJ63_THEAC     1 MEKLNFGIPEWAFEFHGHKCPYMPMGYRAGSYALKIAGLEKEKDHRTYLLSEMSPEDMNGCFNDGAQAATGCTYGKGLFSLLGYGKLALILYRPGRKAIRVHVRNSFMDELSTRASDFFRYRKQGYEPSEIPAGAIDPVLEWISSLEDEEIFEYREIDGFTFEPVKKNGAKVRCDVCGEYTYEADAKLLNGKPVCKPDYYG 201
               SCOP domains d2gvia1 A:1-168 Uncharacterized protein Ta1109                                                                                                                          d2gvia2 A:169-201                 SCOP domains
               CATH domains -2gviA01             2gviA02 A:22-103,A:147-161  [code=3.30.1330.20, no name defined]                  2gviA01 A:2-21,A:104-146 pa2218 like domain2gviA02        ------2gviA03 A:168-201                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eehhhhhhhh...hhhhhhhhhhhhhhhhhh.........eeee........hhhhhhhhhhhh.......eee......eeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhheeeeee.............eee......eee.hhheee..eeehhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gvi A   1 mEKLNFGIPEWAFEFHGHKCPYmPmGYRAGSYALKIAGLEKEKDHRTYLLSEmSPEDmNGCFNDGAQAATGCTYGKGLFSLLGYGKLALILYRPGRKAIRVHVRNSFmDELSTRASDFFRYRKQGYEPSEIPAGAIDPVLEWISSLEDEEIFEYREIDGFTFEPVKKNGAKVRCDVCGEYTYEADAKLLNGKPVCKPDYYG 201
                            |       10        20  | |   30        40        50  |    |60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
                            |                    23-MSE                        53-MSE|                                               108-MSE                                                                                         
                            1-MSE                  25-MSE                           58-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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: FwdE/GAPDH domain-like (188)

Superfamily: FwdE-like (2)

Family: FwdE-like (2)

Protein domain: Uncharacterized protein Ta1109 (1)

Thermoplasma acidophilum [TaxId: 2303] (1)

d2gvia1

A:1-168

Class: Small proteins (3458)

Fold: Glucocorticoid receptor-like (DNA-binding domain) (292)

Superfamily: Glucocorticoid receptor-like (DNA-binding domain) (292)

Family: FwdE C-terminal domain-like (1)

Protein domain: Uncharacterized protein Ta1109 (1)

Thermoplasma acidophilum [TaxId: 2303] (1)

d2gvia2

A:169-201

CATH Domains (3, 3)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.20, no name defined] (18)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

2gviA02

A:22-103,A:147-161

Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1 (140)

Homologous Superfamily: [code=3.30.60.20, no name defined] (15)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

2gviA03

A:168-201

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: pa2218 like fold (1)

Homologous Superfamily: pa2218 like domain (1)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

2gviA01

A:2-21,A:104-146

Pfam Domains (0, 0)

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

Gene Ontology (1, 1)

Asymmetric Unit(hide GO term definitions)

Chain A (Q9HJ63_THEAC | Q9HJ63)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 26)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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