1V25 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TT0168 FROM THERMUS THERMOPHILUS HB8

Authors :   Y. Hisanaga, H. Ago, T. Nakatsu, K. Hamada, K. Ida, H. Kanda, M. Yamamoto, T. Hori, Y. Arii, M. Sugahara, S. Kuramitsu, S. Yokoyama, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   07 Oct 03 (Deposition) - 27 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Ligase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Hisanaga, H. Ago, N. Nakagawa, K. Hamada, K. Ida, M. Yamamoto, T. Hori, Y. Arii, M. Sugahara, S. Kuramitsu, S. Yokoyama, M. Miyano
Structural Basis Of The Substrate-Specific Two-Step Catalysis Of Long Chain Fatty Acyl-Coa Synthetase Dimer
J. Biol. Chem. V. 279 31717 2004
PubMed-ID: 15145952 | Reference-DOI: 10.1074/JBC.M400100200
(for further references see the PDB file header)

Molecule 1 - LONG-CHAIN-FATTY-ACID-COA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.2.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:184 , GLU A:328 , ANP A:666 , HOH A:1120	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	THR B:184 , GLU B:328 , ANP B:1666	BINDING SITE FOR RESIDUE MG B 1002
3	AC3	SOFTWARE	PHE A:229 , HIS A:230 , VAL A:231 , TRP A:234 , GLY A:302 , SER A:303 , ALA A:304 , GLN A:322 , GLY A:323 , TYR A:324 , GLY A:325 , LEU A:326 , THR A:327 , ASP A:418 , ARG A:433 , LYS A:435 , LYS A:439 , TRP A:444 , MG A:1001 , HOH A:1034 , HOH A:1098 , HOH A:1191 , HOH A:1196 , HOH A:1226	BINDING SITE FOR RESIDUE ANP A 666
4	AC4	SOFTWARE	PHE B:229 , HIS B:230 , VAL B:231 , TRP B:234 , GLY B:302 , SER B:303 , ALA B:304 , GLN B:322 , GLY B:323 , TYR B:324 , GLY B:325 , LEU B:326 , THR B:327 , ASP B:418 , ARG B:433 , LYS B:435 , LYS B:439 , TRP B:444 , MG B:1002 , HOH B:1725 , HOH B:1733 , HOH B:1734 , HOH B:1739 , HOH B:1787 , HOH B:1801 , HOH B:1859	BINDING SITE FOR RESIDUE ANP B 1666

(no "SS Bond" information available for 1V25)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:330	-	Pro A:331
2	Ser B:330	-	Pro B:331

(no "SAP(SNP)/Variant" information available for 1V25)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMP_BINDING	PS00455	Putative AMP-binding domain signature.	LCFCS_THET8	181-192	2	A:181-192 B:181-192

(no "Exon" information available for 1V25)

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:491
 aligned with LCFCS_THET8 | Q5SKN9 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:534
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537    
          LCFCS_THET8     8 AFPSTMMDEELNLWDFLERAAALFGRKEVVSRLHTGEVHRTTYAEVYQRARRLMGGLRALGVGVGDRVATLGFNHFRHLEAYFAVPGMGAVLHTANPRLSPKEIAYILNHAEDKVLLFDPNLLPLVEAIRGELKTVQHFVVMDEKAPEGYLAYEEALGEEADPVRVPERAACGMAYTTGTTGLPKGVVYSHRALVLHSLAASLVDGTALSEKDVVLPVVPMFHVNAWCLPYAATLVGAKQVLPGPRLDPASLVELFDGEGVTFTAGVPTVWLALADYLESTGHRLKTLRRLVVGGSAAPRSLIARFERMGVEVRQGYGLTETSPVVVQNFVKSHLESLSEEEKLTLKAKTGLPIPLVRLRVADEEGRPVPKDGKALGEVQLKGPWITGGYYGNEEATRSALTPDGFFRTGDIAVWDEEGYVEIKDRLKDLIKSGGEWISSVDLENALMGHPKVKEAAVVAIPHPKWQERPLAVVVPRGEKPTPEELNEHLLKAGFAKWQLPDAYVFAEEIPRTSAGKFLKRALREQYKNYYGGA 541
               SCOP domains d1v25a_ A: Long chain fatty acid-CoA ligase TT0168                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eeee.........eehhhhh.............eeeeeee.......eeeeeehhhhhhhhhhh............eeee.....hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhh..eeeeeee.hhhh.eeee...hhhhh..hhhhhhhhhh...ee....eeeee..............eeeeee..........hhhhhhh.......eeeeeeeee.....eeeeee...eeee..eeeehhhhhh.----------.eeeee.....eeeee..-------------------...........--------------...hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v25 A   8 AFPSTMMDEELNLWDFLERAAALFGRKEVVSRLHTGEVHRTTYAEVYQRARRLMGGLRALGVGVGDRVATLGFNHFRHLEAYFAVPGMGAVLHTANPRLSPKEIAYILNHAEDKVLLFDPNLLPLVEAIRGELKTVQHFVVMDEKAPEGYLAYEEALGEEADPVRVPERAACGMAYTTGTTGLPKGVVYSHRALVLHSLAASLVDGTALSEKDVVLPVVPMFHVNAWCLPYAATLVGAKQVLPGPRLDPASLVELFDGEGVTFTAGVPTVWLALADYLESTGHRLKTLRRLVVGGSAAPRSLIARFERMGVEVRQGYGLTETSPVVVQNFVKSHLESLSEEEKLTLKAKTGLPIPLVRLRVADEEGRPVPKDGKALGEVQLKGPWITGGYYGNEEATRSALTPDGFFRTGDIAVWDEEGYVEIKDRLKDLIKSGGEWISSVDLENA----------AVVAIPHPKWQERPLAVV-------------------GFAKWQLPDAY--------------LKRALREQYKNYYGGA 541
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447     |   -      |467       477   |     -         -   |   507   |     -       527       537    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       453        464              481                 501       511            526

Chain B from PDB  Type:PROTEIN  Length:507
 aligned with LCFCS_THET8 | Q5SKN9 from UniProtKB/Swiss-Prot  Length:541

    Alignment length:534
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537    
          LCFCS_THET8     8 AFPSTMMDEELNLWDFLERAAALFGRKEVVSRLHTGEVHRTTYAEVYQRARRLMGGLRALGVGVGDRVATLGFNHFRHLEAYFAVPGMGAVLHTANPRLSPKEIAYILNHAEDKVLLFDPNLLPLVEAIRGELKTVQHFVVMDEKAPEGYLAYEEALGEEADPVRVPERAACGMAYTTGTTGLPKGVVYSHRALVLHSLAASLVDGTALSEKDVVLPVVPMFHVNAWCLPYAATLVGAKQVLPGPRLDPASLVELFDGEGVTFTAGVPTVWLALADYLESTGHRLKTLRRLVVGGSAAPRSLIARFERMGVEVRQGYGLTETSPVVVQNFVKSHLESLSEEEKLTLKAKTGLPIPLVRLRVADEEGRPVPKDGKALGEVQLKGPWITGGYYGNEEATRSALTPDGFFRTGDIAVWDEEGYVEIKDRLKDLIKSGGEWISSVDLENALMGHPKVKEAAVVAIPHPKWQERPLAVVVPRGEKPTPEELNEHLLKAGFAKWQLPDAYVFAEEIPRTSAGKFLKRALREQYKNYYGGA 541
               SCOP domains d1v25b_ B: Long chain fatty acid-CoA ligase TT0168                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhh...eeeee.....eeeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...eeee...hhhhhhhhhhhh....eeee.........eehhhhh.............eeeeeee.......eeeeeehhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhh...eeeeeee.hhhh.eeee...hhhhh..hhhhhhhhhhh..ee....eeeee..............eeeeee..........hhhhhhhh......eeeeeeeee.....eeeeee...eeee..eeeehhhhhhhhh..-----.eeeee.......eeeee-------------hhhhhhh..hhhhh..ee..---------...hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v25 B   8 AFPSTMMDEELNLWDFLERAAALFGRKEVVSRLHTGEVHRTTYAEVYQRARRLMGGLRALGVGVGDRVATLGFNHFRHLEAYFAVPGMGAVLHTANPRLSPKEIAYILNHAEDKVLLFDPNLLPLVEAIRGELKTVQHFVVMDEKAPEGYLAYEEALGEEADPVRVPERAACGMAYTTGTTGLPKGVVYSHRALVLHSLAASLVDGTALSEKDVVLPVVPMFHVNAWCLPYAATLVGAKQVLPGPRLDPASLVELFDGEGVTFTAGVPTVWLALADYLESTGHRLKTLRRLVVGGSAAPRSLIARFERMGVEVRQGYGLTETSPVVVQNFVKSHLESLSEEEKLTLKAKTGLPIPLVRLRVADEEGRPVPKDGKALGEVQLKGPWITGGYYGNEEATRSALTPDGFFRTGDIAVWDEEGYVEIKDRLKDLIKSGGEWISSVDLENALMGH-----AAVVAIPHPKWQERPLAV-------------NEHLLKAGFAKWQLPDAYVF---------GKFLKRALREQYKNYYGGA 541
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457     | 467       477  |      -      |497       507     |   -     | 527       537    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           457   463              480           494                513       523

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Acetyl-CoA synthetase-like (64)

Superfamily: Acetyl-CoA synthetase-like (64)

Family: Acetyl-CoA synthetase-like (38)

Protein domain: Long chain fatty acid-CoA ligase TT0168 (3)

Thermus thermophilus [TaxId: 274] (3)

1a	d1v25a_	A:
1b	d1v25b_	B:

(no "CATH Domain" information available for 1V25)

(no "Pfam Domain" information available for 1V25)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LCFCS_THET8 | Q5SKN9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0004467	long-chain fatty acid-CoA ligase activity	Catalysis of the reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0001676	long-chain fatty acid metabolic process	The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:330 - Pro A:331	[ RasMol ]
		Ser B:330 - Pro B:331	[ RasMol ]

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	1v25
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UniProtKB/Swiss-Prot
	LCFCS_THET8 \| Q5SKN9	:	1ult 1v26

1v26	THE SAME PROTEIN WITH THE LIGAND AMM RELATED ID: TTK003000168.2 RELATED DB: TARGETDB

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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