1UF9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TT1252 FROM THERMUS THERMOPHILUS

Authors :   A. Seto, K. Murayama, M. Toyama, A. Ebihara, N. Nakagawa, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 May 03 (Deposition) - 28 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   P-Loop, Nucleotide Binding Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Seto, K. Murayama, M. Toyama, A. Ebihara, N. Nakagawa, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Atp-Induced Structural Change Of Dephosphocoenzyme A Kinase From Thermus Thermophilus Hb8
Proteins V. 58 235 2005
PubMed-ID: 15526298 | Reference-DOI: 10.1002/PROT.20276
(for further references see the PDB file header)

Molecule 1 - TT1252 PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEOTIDE BINDING DOMAIN
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:20 , LYS B:21 , SER B:22 , ARG B:145	BINDING SITE FOR RESIDUE PO4 B 600
2	AC2	SOFTWARE	ASN C:16 , ILE C:17 , GLY C:18 , SER C:19 , GLY C:20 , LYS C:21 , SER C:22 , THR C:23 , ARG C:141 , ARG C:145 , ASN C:176 , THR C:177	BINDING SITE FOR RESIDUE ATP C 500

(no "SS Bond" information available for 1UF9)

(no "Cis Peptide Bond" information available for 1UF9)

(no "SAP(SNP)/Variant" information available for 1UF9)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPCK	PS51219	Dephospho-CoA kinase (DPCK) domain profile.	COAE_THET8	10-203	3	A:10-196 B:10-196 C:10-196

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPCK	PS51219	Dephospho-CoA kinase (DPCK) domain profile.	COAE_THET8	10-203	1	A:10-196 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPCK	PS51219	Dephospho-CoA kinase (DPCK) domain profile.	COAE_THET8	10-203	1	- B:10-196 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPCK	PS51219	Dephospho-CoA kinase (DPCK) domain profile.	COAE_THET8	10-203	1	- - C:10-196

(no "Exon" information available for 1UF9)

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:191
 aligned with COAE_THET8 | Q56416 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
           COAE_THET8     6 KHPIIIGITGNIGSGKSTVAALLRSWGYPVLDLDALAARARENKEEELKRLFPEAVVGGRLDRRALARLVFSDPERLKALEAVVHPEVRRLLMEELSRLEAPLVFLEIPLLFEKGWEGRLHGTLLVAAPLEERVRRVMARSGLSREEVLARERAQMPEEEKRKRATWVLENTGSLEDLERALKAVLAELTG 196
               SCOP domains d1uf9a_ A: Dephospho-CoA kinase                                                                                                                                                                 SCOP domains
               CATH domains 1uf9A00 A:6-196 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhh.eeeee..hhhhhhhhhhh.....hhhhhhhhh...hhhhhhhhh.eee...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DPCK  PDB: A:10-196 UniProt: 10-203                                                                                                                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uf9 A   6 KHPIIIGITGNIGSGKSTVAALLRSWGYPVLDLDALAARARENKEEELKRLFPEAVVGGRLDRRALARLVFSDPERLKALEAVVHPEVRRLLmEELSRLEAPLVFLEIPLLFEKGWEGRLHGTLLVAAPLEERVRRVmARSGLSREEVLARERAQmPEEEKRKRATWVLENTGSLEDLERALKAVLAELTG 196
                                    15        25        35        45        55        65        75        85        95  |    105       115       125       135       145       155     | 165       175       185       195 
                                                                                                                       98-MSE                                      143-MSE           161-MSE

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with COAE_THET8 | Q56416 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
           COAE_THET8     6 KHPIIIGITGNIGSGKSTVAALLRSWGYPVLDLDALAARARENKEEELKRLFPEAVVGGRLDRRALARLVFSDPERLKALEAVVHPEVRRLLMEELSRLEAPLVFLEIPLLFEKGWEGRLHGTLLVAAPLEERVRRVMARSGLSREEVLARERAQMPEEEKRKRATWVLENTGSLEDLERALKAVLAELTG 196
               SCOP domains d1uf9b_ B: Dephospho-CoA kinase                                                                                                                                                                 SCOP domains
               CATH domains 1uf9B00 B:6-196 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhh.eeeee..hhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhh.eee...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DPCK  PDB: B:10-196 UniProt: 10-203                                                                                                                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uf9 B   6 KHPIIIGITGNIGSGKSTVAALLRSWGYPVLDLDALAARARENKEEELKRLFPEAVVGGRLDRRALARLVFSDPERLKALEAVVHPEVRRLLmEELSRLEAPLVFLEIPLLFEKGWEGRLHGTLLVAAPLEERVRRVmARSGLSREEVLARERAQmPEEEKRKRATWVLENTGSLEDLERALKAVLAELTG 196
                                    15        25        35        45        55        65        75        85        95  |    105       115       125       135       145       155     | 165       175       185       195 
                                                                                                                       98-MSE                                      143-MSE           161-MSE

Chain C from PDB  Type:PROTEIN  Length:191
 aligned with COAE_THET8 | Q56416 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:191
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
           COAE_THET8     6 KHPIIIGITGNIGSGKSTVAALLRSWGYPVLDLDALAARARENKEEELKRLFPEAVVGGRLDRRALARLVFSDPERLKALEAVVHPEVRRLLMEELSRLEAPLVFLEIPLLFEKGWEGRLHGTLLVAAPLEERVRRVMARSGLSREEVLARERAQMPEEEKRKRATWVLENTGSLEDLERALKAVLAELTG 196
               SCOP domains d1uf9c_ C: Dephospho-CoA kinase                                                                                                                                                                 SCOP domains
               CATH domains 1uf9C00 C:6-196 P-loop containing nucleotide triphosphate hydrolases                                                                                                                            CATH domains
           Pfam domains (1) ---CoaE-1uf9C01 C:9-182                                                                                                                                                          -------------- Pfam domains (1)
           Pfam domains (2) ---CoaE-1uf9C02 C:9-182                                                                                                                                                          -------------- Pfam domains (2)
           Pfam domains (3) ---CoaE-1uf9C03 C:9-182                                                                                                                                                          -------------- Pfam domains (3)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..............eeeee..hhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhh...eee...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DPCK  PDB: C:10-196 UniProt: 10-203                                                                                                                                                         PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uf9 C   6 KHPIIIGITGNIGSGKSTVAALLRSWGYPVLDLDALAARARENKEEELKRLFPEAVVGGRLDRRALARLVFSDPERLKALEAVVHPEVRRLLmEELSRLEAPLVFLEIPLLFEKGWEGRLHGTLLVAAPLEERVRRVmARSGLSREEVLARERAQmPEEEKRKRATWVLENTGSLEDLERALKAVLAELTG 196
                                    15        25        35        45        55        65        75        85        95  |    105       115       125       135       145       155     | 165       175       185       195 
                                                                                                                       98-MSE                                      143-MSE           161-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: Nucleotide and nucleoside kinases (231)

Protein domain: Dephospho-CoA kinase (8)

Thermus thermophilus [TaxId: 274] (1)

1a	d1uf9a_	A:
1b	d1uf9b_	B:
1c	d1uf9c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

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

Thermus thermophilus. Organism_taxid: 274. (6)

1a	1uf9A00	A:6-196
1b	1uf9B00	B:6-196
1c	1uf9C00	C:6-196

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: CoaE (7)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (1)

1a	CoaE-1uf9C01	C:9-182
1b	CoaE-1uf9C02	C:9-182
1c	CoaE-1uf9C03	C:9-182

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (COAE_THET8 | Q56416)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004140	dephospho-CoA kinase activity	Catalysis of the reaction: 3'-dephospho-CoA + ATP = ADP + CoA + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	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:0015937	coenzyme A biosynthetic process	The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uf9)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1uf9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	COAE_THET8 \| Q56416
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	COAE_THET8 \| Q56416
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1UF9)

(no "Related Entries Specified in the PDB File" available for 1UF9)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File