2UX9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN R65A MUTANT

Authors :   B. Meissner, L. -O. Essen

Date :   27 Mar 07 (Deposition) - 11 Sep 07 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (2x)

Keywords :   Flavoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Meissner, E. Schleicher, S. Weber, L. -O. Essen
The Dodecin From Thermus Thermophilus, A Bifunctional Cofactor Storage Protein.
J. Biol. Chem. V. 282 33142 2007
PubMed-ID: 17855371 | Reference-DOI: 10.1074/JBC.M704951200

Molecule 1 - DODECIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)GOLD
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Mutation	:	YES
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	COA	6	Ligand/Ion	COENZYME A
2	FMN	6	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NA	4	Ligand/Ion	SODIUM ION
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 30)

No.	Name	Count	Type	Full Name
1	COA	12	Ligand/Ion	COENZYME A
2	FMN	12	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	FMN A:1069 , HOH A:2062	BINDING SITE FOR RESIDUE NA A1068
02	AC2	SOFTWARE	LYS A:3 , TYR A:5 , ASP A:37 , TRP A:38 , ALA A:65 , NA A:1068 , HOH A:2036 , HOH A:2063 , HOH A:2064 , HOH A:2065 , ARG C:45 , THR C:47 , GLN C:57	BINDING SITE FOR RESIDUE FMN A1069
03	AC3	SOFTWARE	ARG A:28 , THR A:32 , ARG A:34 , HIS A:35 , PHE A:64 , ALA A:65 , GLU A:67 , HOH A:2066 , LYS C:6 , COA C:1074 , HOH C:2080 , HOH C:2088 , LYS E:6 , VAL E:8 , LEU E:10 , ALA E:29 , LEU E:66 , COA E:1071	BINDING SITE FOR RESIDUE COA A1070
04	AC4	SOFTWARE	GLU B:9 , GLU B:43 , LYS F:7 , LYS F:42 , GLU F:61	BINDING SITE FOR RESIDUE PO4 B1069
05	AC5	SOFTWARE	LYS B:3 , TYR B:5 , ASP B:37 , TRP B:38 , ALA B:65 , HOH B:2084 , HOH B:2085 , HOH B:2086 , ARG D:45 , THR D:47 , GLN D:57	BINDING SITE FOR RESIDUE FMN B1070
06	AC6	SOFTWARE	GLU A:15 , GLU A:16 , ALA A:51 , LYS A:54 , HOH A:2055 , ARG B:28 , THR B:32 , LEU B:33 , ARG B:34 , HIS B:35 , PHE B:64 , ALA B:65 , GLU B:67 , HOH B:2087 , HOH B:2089 , HOH B:2090 , HOH B:2091 , HOH B:2092 , HOH B:2093 , LYS D:6 , LEU D:66 , COA D:1071 , LYS F:6 , VAL F:8 , ALA F:29 , LEU F:33 , PHE F:64 , LEU F:66 , COA F:1071 , HOH F:2087	BINDING SITE FOR RESIDUE COA B1071
07	AC7	SOFTWARE	LYS A:7 , LYS A:42 , GLU A:61 , GLU C:9 , LYS C:42 , GLU C:43	BINDING SITE FOR RESIDUE PO4 C1070
08	AC8	SOFTWARE	HOH A:2006 , GLU C:55 , HOH C:2062 , HOH C:2063	BINDING SITE FOR RESIDUE NA C1071
09	AC9	SOFTWARE	ASP C:37 , FMN C:1073 , HOH C:2044 , HOH C:2077 , HOH C:2079	BINDING SITE FOR RESIDUE NA C1072
10	BC1	SOFTWARE	LYS C:3 , TYR C:5 , ASP C:37 , TRP C:38 , ALA C:65 , NA C:1072 , HOH C:2076 , HOH C:2077 , HOH C:2078 , HOH C:2079 , FMN D:1070 , GLN E:57 , ARG F:45 , THR F:47 , GLN F:57	BINDING SITE FOR RESIDUE FMN C1073
11	BC2	SOFTWARE	LYS A:6 , VAL A:8 , LEU A:10 , ALA A:29 , LEU A:66 , COA A:1070 , HOH A:2066 , ARG C:28 , THR C:32 , LEU C:33 , ARG C:34 , PHE C:64 , ALA C:65 , LEU C:66 , GLU C:67 , HOH C:2080 , HOH C:2081 , HOH C:2082 , HOH C:2083 , HOH C:2084 , HOH C:2085 , HOH C:2086 , HOH C:2087 , HOH C:2088 , HOH C:2089 , HOH C:2090 , HOH D:2045 , LYS E:6 , GLU E:50 , LEU E:66 , COA E:1071 , HOH E:2064	BINDING SITE FOR RESIDUE COA C1074
12	BC3	SOFTWARE	FMN C:1073 , LYS D:3 , TYR D:5 , ASP D:37 , TRP D:38 , HOH D:2047 , HOH D:2076 , HOH D:2077 , THR E:32 , ARG E:45 , THR E:47 , GLN E:57 , HOH E:2046 , GLN F:57	BINDING SITE FOR RESIDUE FMN D1070
13	BC4	SOFTWARE	LYS B:6 , VAL B:8 , LEU B:10 , ARG B:28 , LEU B:66 , COA B:1071 , ARG D:28 , THR D:32 , LEU D:33 , ARG D:34 , HIS D:35 , PHE D:64 , ALA D:65 , GLU D:67 , HOH D:2078 , HOH D:2079 , HOH D:2080 , LYS F:6 , COA F:1071 , HOH F:2086	BINDING SITE FOR RESIDUE COA D1071
14	BC5	SOFTWARE	GLN A:57 , ARG B:45 , THR B:47 , GLN B:57 , LYS E:3 , TYR E:5 , ASP E:37 , TRP E:38 , ALA E:65 , FMN E:1070 , HOH E:2080 , HOH E:2081 , HOH E:2083	BINDING SITE FOR RESIDUE FMN E1069
15	BC6	SOFTWARE	ARG A:45 , THR A:47 , GLN A:57 , GLN B:57 , HOH B:2074 , FMN E:1069 , NA E:1072 , HOH E:2084 , HOH E:2085 , LYS F:3 , TYR F:5 , ASP F:37 , TRP F:38 , ALA F:65	BINDING SITE FOR RESIDUE FMN E1070
16	BC7	SOFTWARE	LYS A:6 , LEU A:66 , COA A:1070 , LYS C:6 , VAL C:8 , ALA C:29 , LEU C:33 , LEU C:66 , COA C:1074 , HOH C:2086 , HOH C:2087 , THR E:32 , LEU E:33 , ARG E:34 , HIS E:35 , ALA E:65 , GLU E:67 , HOH E:2086	BINDING SITE FOR RESIDUE COA E1071
17	BC8	SOFTWARE	LYS D:7 , LYS D:42 , HOH D:2049 , GLU F:9 , LYS F:42 , GLU F:43	BINDING SITE FOR RESIDUE PO4 F1070
18	BC9	SOFTWARE	SER A:14 , GLU A:15 , GLU A:16 , HOH A:2014 , LYS B:6 , LEU B:66 , COA B:1071 , LYS D:6 , VAL D:8 , LEU D:66 , COA D:1071 , GLY E:2 , ARG F:28 , THR F:32 , LEU F:33 , ARG F:34 , HIS F:35 , PHE F:64 , ALA F:65 , LEU F:66 , GLU F:67 , HOH F:2085 , HOH F:2086 , HOH F:2087 , HOH F:2088 , HOH F:2089 , HOH F:2090 , HOH F:2092	BINDING SITE FOR RESIDUE COA F1071
19	CC1	SOFTWARE	FMN E:1070 , HOH F:2007 , HOH F:2050	BINDING SITE FOR RESIDUE NA E1072

(no "SS Bond" information available for 2UX9)

(no "Cis Peptide Bond" information available for 2UX9)

(no "SAP(SNP)/Variant" information available for 2UX9)

(no "PROSITE Motif" information available for 2UX9)

(no "Exon" information available for 2UX9)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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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:66
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:66
                                    11        21        31        41        51        61      
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLE 67
               SCOP domains d2ux9a1 A:2-67 Uncharacterized protein TTHA1431                    SCOP domains
               CATH domains 2ux9A00 A:2-67 Flavin-binding protein dodecin                      CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2ux9 A  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFALE 67
                                    11        21        31        41        51        61

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:67
                                    11        21        31        41        51        61       
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
               SCOP domains d2ux9b_ B: automated matches                                        SCOP domains
               CATH domains 2ux9B00 B:2-68 Flavin-binding protein dodecin                       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2ux9 B  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFALEE 68
                                    11        21        31        41        51        61

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2ux9c_ C: automated matches                                         SCOP domains
               CATH domains 2ux9C00 C:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2ux9 C  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFALEET 69
                                    11        21        31        41        51        61

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2ux9d_ D: automated matches                                         SCOP domains
               CATH domains 2ux9D00 D:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2ux9 D  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFALEET 69
                                    11        21        31        41        51        61

Chain E from PDB  Type:PROTEIN  Length:67
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:67
                                    11        21        31        41        51        61       
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEE 68
               SCOP domains d2ux9e_ E: automated matches                                        SCOP domains
               CATH domains 2ux9E00 E:2-68 Flavin-binding protein dodecin                       CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                  2ux9 E  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFALEE 68
                                    11        21        31        41        51        61

Chain F from PDB  Type:PROTEIN  Length:68
 aligned with DODEC_THET8 | Q5SIE3 from UniProtKB/Swiss-Prot  Length:69

    Alignment length:68
                                    11        21        31        41        51        61        
           DODEC_THET8    2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET 69
               SCOP domains d2ux9f_ F: automated matches                                         SCOP domains
               CATH domains 2ux9F00 F:2-69 Flavin-binding protein dodecin                        CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  2ux9 F  2 GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFALEET 69
                                    11        21        31        41        51        61

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Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Dodecin subunit-like (56)

Superfamily: Dodecin-like (33)

Family: Dodecin-like (29)

Protein domain: automated matches (24)

Thermus thermophilus HB8 [TaxId: 300852] (6)

1a	d2ux9b_	B:
1b	d2ux9c_	C:
1c	d2ux9d_	D:
1d	d2ux9e_	E:
1e	d2ux9f_	F:

Protein domain: Uncharacterized protein TTHA1431 (3)

Thermus thermophilus [TaxId: 274] (3)

d2ux9a1

A:2-67

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dodecin subunit-like (24)

Homologous Superfamily: Flavin-binding protein dodecin (24)

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. (5)

1a	2ux9B00	B:2-68
1b	2ux9E00	E:2-68
1c	2ux9C00	C:2-69
1d	2ux9D00	D:2-69
1e	2ux9F00	F:2-69
1f	2ux9A00	A:2-67

(no "Pfam Domain" information available for 2UX9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (DODEC_THET8 | Q5SIE3)

molecular function
	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.

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	2ux9
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	DODEC_THET8 \| Q5SIE3	:	2cz8 2deg 2v18 2v19 2v21 2vyx

2v18	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN
2v19	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN R45A MUTANT
2v21	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS DODECIN IN COMPLEX WITH PREBOUND FMN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (2, 6)

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