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Title :   2.1 A STRUCTURE OF ACYL-ADENYLATE SYNTHETASE FROM METHANOSARCINA ACETIVORANS CONTAINING A LINK BETWEEN LYS256 AND CYS298

Authors :   M. B. Shah, A. M. Gulick, K. S. Smith, C. Ingram-Smith

Date :   07 Oct 08 (Deposition) - 07 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Adenylate-Forming Acyl-Coa Synthetase Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. B. Shah, C. Ingram-Smith, L. L. Cooper, J. Qu, Y. Meng, K. S. Smith, A. M. Gulick
The 2. 1 A Crystal Structure Of An Acyl-Coa Synthetase From Methanosarcina Acetivorans Reveals An Alternate Acyl-Bindin Pocket For Small Branched Acyl Substrates.
Proteins V. 77 685 2009
PubMed-ID: 19544569 | Reference-DOI: 10.1002/PROT.22482

Molecule 1 - AMP-BINDING PROTEIN
	Chains	:	A, B
	EC Number	:	6.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTABLUE (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET19B
	Fragment	:	UNP RESIDUES 4-560
	Gene	:	MA_2912, METHANOSARCINA ACETIVORANS
	Organism Scientific	:	METHANOSARCINA ACETIVORANS
	Organism Taxid	:	2214

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 21)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EPE	3	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	FOR	2	Mod. Residue	FORMYL GROUP
4	GOL	7	Ligand/Ion	GLYCEROL
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	NO3	2	Ligand/Ion	NITRATE ION
7	PGE	3	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 1 (6, 19)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EPE	3	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	FOR	2	Mod. Residue	FORMYL GROUP
4	GOL	7	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO3	2	Ligand/Ion	NITRATE ION
7	PGE	3	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 2 (6, 11)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	FOR	1	Mod. Residue	FORMYL GROUP
4	GOL	4	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO3	1	Ligand/Ion	NITRATE ION
7	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL

Biological Unit 3 (5, 8)

No.	Name	Count	Type	Full Name
1	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3	FOR	1	Mod. Residue	FORMYL GROUP
4	GOL	3	Ligand/Ion	GLYCEROL
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO3	1	Ligand/Ion	NITRATE ION
7	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:237 , GLN A:238 , THR A:248 , LYS A:256 , CYS A:298	BINDING SITE FOR RESIDUE FOR A 999
02	AC2	SOFTWARE	ASP A:57 , ASN A:284 , GLU A:287 , LYS A:288	BINDING SITE FOR RESIDUE PGE A 991
03	AC3	SOFTWARE	TRP A:254 , LYS A:256 , GLY A:327 , PHE A:350 , GLY A:351 , THR A:353 , LYS A:456 , GLY A:459 , LYS A:461 , GOL A:1005 , HOH A:1205	BINDING SITE FOR RESIDUE 1PE A 994
04	AC4	SOFTWARE	ASN A:512 , ASP A:516 , LYS A:519 , TYR A:527 , GLY B:394 , GLU B:396	BINDING SITE FOR RESIDUE 1PE A 995
05	AC5	SOFTWARE	SER A:97 , TYR A:247 , THR A:248 , VAL A:249 , ALA A:250 , LYS A:261 , VAL A:274 , TYR A:275 , TYR A:277 , ASP A:278 , HOH A:1179 , HOH A:1203 , GLU B:392	BINDING SITE FOR RESIDUE EPE A 996
06	AC6	SOFTWARE	VAL A:413 , TRP A:426 , HIS A:427 , ASP A:428 , GLY A:429 , TYR A:430 , GLU B:132 , CYS B:158	BINDING SITE FOR RESIDUE EPE A 997
07	AC7	SOFTWARE	HOH A:1193 , HOH A:1194 , HOH A:1195 , HOH A:1196 , HOH B:1414 , HOH B:1415	BINDING SITE FOR RESIDUE MG A 1000
08	AC8	SOFTWARE	ARG A:125 , ASP A:126 , ARG A:130 , PHE A:216 , GLU A:466 , THR A:522 , LYS A:526 , HOH A:1024	BINDING SITE FOR RESIDUE NO3 A 1001
09	AC9	SOFTWARE	ILE A:26 , PRO A:377 , GLY A:378 , TYR A:379 , PRO A:408 , VAL A:409	BINDING SITE FOR RESIDUE GOL A 1002
10	BC1	SOFTWARE	GLU A:328 , PRO A:329 , GLU A:348 , PHE A:350 , ILE A:372 , PHE A:447 , LYS A:456 , HOH A:1042 , HOH A:1043 , HOH A:1129 , HOH A:1134	BINDING SITE FOR RESIDUE GOL A 1003
11	BC2	SOFTWARE	SER A:210 , SER A:211 , LYS A:218 , GLU A:354 , TYR A:415 , ARG A:421 , LYS A:461 , HOH A:1028 , HOH A:1188 , HOH A:1189	BINDING SITE FOR RESIDUE GOL A 1004
12	BC3	SOFTWARE	PHE A:209 , TRP A:254 , GLY A:255 , THR A:353 , 1PE A:994 , HOH A:1169	BINDING SITE FOR RESIDUE GOL A 1005
13	BC4	SOFTWARE	TRP B:237 , GLN B:238 , THR B:248 , LYS B:256 , CYS B:298	BINDING SITE FOR RESIDUE FOR B 999
14	BC5	SOFTWARE	ASP B:57 , ASN B:284 , GLU B:287 , LYS B:288	BINDING SITE FOR RESIDUE PGE B 992
15	BC6	SOFTWARE	TRP B:259 , PHE B:350 , GLY B:351 , THR B:353 , GOL B:1003 , GOL B:1004	BINDING SITE FOR RESIDUE PGE B 993
16	BC7	SOFTWARE	GLU A:392 , SER B:97 , TYR B:247 , THR B:248 , VAL B:249 , ALA B:250 , LYS B:261 , VAL B:274 , TYR B:275 , TYR B:277 , ASP B:278 , HOH B:1237 , HOH B:1306	BINDING SITE FOR RESIDUE EPE B 998
17	BC8	SOFTWARE	HOH A:1198 , HOH A:1199 , HOH B:1419	BINDING SITE FOR RESIDUE MG B 1000
18	BC9	SOFTWARE	ARG B:125 , ASP B:126 , ARG B:130 , PHE B:216 , PRO B:217 , GLU B:466 , THR B:522 , LYS B:526	BINDING SITE FOR RESIDUE NO3 B 1001
19	CC1	SOFTWARE	SER B:210 , SER B:211 , GLY B:212 , GLU B:354 , TYR B:415 , ARG B:421 , HOH B:1135 , HOH B:1320 , HOH B:1409	BINDING SITE FOR RESIDUE GOL B 1002
20	CC2	SOFTWARE	GLU B:328 , GLU B:348 , ILE B:372 , PHE B:447 , PGE B:993 , HOH B:1131 , HOH B:1192 , HOH B:1194	BINDING SITE FOR RESIDUE GOL B 1003
21	CC3	SOFTWARE	GLY B:351 , GLN B:352 , ASP B:435 , PHE B:447 , ARG B:450 , LYS B:461 , PGE B:993	BINDING SITE FOR RESIDUE GOL B 1004

(no "SS Bond" information available for 3ETC)

(no "Cis Peptide Bond" information available for 3ETC)

(no "SAP(SNP)/Variant" information available for 3ETC)

(no "PROSITE Motif" information available for 3ETC)

(no "Exon" information available for 3ETC)

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:531
 aligned with Q8TLW1_METAC | Q8TLW1 from UniProtKB/TrEMBL  Length:560

    Alignment length:534
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535    
         Q8TLW1_METAC     6 SLLSQFVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYARDSPEKLAMIWCDDYGNEKIFTFKDLKYYSDKAANFFVKHGIGKGDYVMLTLKSRYDFWYCMLGLHKLGAIAVPATHMLKTRDIVYRIEKAGLKMIVCIAEDDVPEQVDEAHAECGDIPLKKAKVGGDVLEGWIDFRKELEESSPIFERPTGEVSTKNEDICLVYFSSGTAGFPKMVEHDNTYPLGHILTAKYWQNVEDDGLHYTVADSGWGKCVWGKLYGQWIAGCAVFVYDYDRFEAKNMLEKASKYGVTTFCAPPTIYRFLIKEDLSHYNFSTLKYAVVAGEPLNPEVFNRFLEFTGIKLMEGFGQTETVVTIATFPWMEPKPGSIGKPTPGYKIELMDRDGRLCEVGEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHDGYYHTGDMAWMDEDGYLWFVGRADDIIKTSGYKVGPFEVESALIQHPAVLECAITGVPDPVRGQVIKATIVLTKDYTPSDSLKNELQDHVKNVTAPYKYPRIIEFVPE 539
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh......hhhhhhhhh........hhhhhhhhhhhhhh...eeeeeee....eeeeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh....eeeee........eehhhhhhhh.......hhhhh.....eeeeeee.......eeeeee.hhhhhhhhhhhh........eeee......hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh..eeeehhhhhhhhhh...---......eeee.....hhhhhhhhhhhhh...eeee........ee.............ee....eeeee............eeeeee...........ee..hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3etc A   3 SLLSQFVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYARDSPEKLAMIWCDDYGNEKIFTFKDLKYYSDKAANFFVKHGIGKGDYVMLTLKSRYDFWYCMLGLHKLGAIAVPATHMLKTRDIVYRIEKAGLKMIVCIAEDDVPEQVDEAHAECGDIPLKKAKVGGDVLEGWIDFRKELEESSPIFERPTGEVSTKNEDICLVYFSSGTAGFPKMVEHDNTYPLGHILTAKYWQNVEDDGLHYTVADSGWGKCVWGKLYGQWIAGCAVFVYDYDRFEAKNMLEKASKYGVTTFCAPPTIYRFLIKEDL---NFSTLKYAVVAGEPLNPEVFNRFLEFTGIKLMEGFGQTETVVTIATFPWMEPKPGSIGKPTPGYKIELMDRDGRLCEVGEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHDGYYHTGDMAWMDEDGYLWFVGRADDIIKTSGYKVGPFEVESALIQHPAVLECAITGVPDPVRGQVIKATIVLTKDYTPSDSLKNELQDHVKNVTAPYKYPRIIEFVPE 536
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312   |   322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532    
                                                                                                                                                                                                                                                                                                                                               312 316

Chain B from PDB  Type:PROTEIN  Length:537
 aligned with Q8TLW1_METAC | Q8TLW1 from UniProtKB/TrEMBL  Length:560

    Alignment length:537
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       
         Q8TLW1_METAC     6 SLLSQFVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYARDSPEKLAMIWCDDYGNEKIFTFKDLKYYSDKAANFFVKHGIGKGDYVMLTLKSRYDFWYCMLGLHKLGAIAVPATHMLKTRDIVYRIEKAGLKMIVCIAEDDVPEQVDEAHAECGDIPLKKAKVGGDVLEGWIDFRKELEESSPIFERPTGEVSTKNEDICLVYFSSGTAGFPKMVEHDNTYPLGHILTAKYWQNVEDDGLHYTVADSGWGKCVWGKLYGQWIAGCAVFVYDYDRFEAKNMLEKASKYGVTTFCAPPTIYRFLIKEDLSHYNFSTLKYAVVAGEPLNPEVFNRFLEFTGIKLMEGFGQTETVVTIATFPWMEPKPGSIGKPTPGYKIELMDRDGRLCEVGEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHDGYYHTGDMAWMDEDGYLWFVGRADDIIKTSGYKVGPFEVESALIQHPAVLECAITGVPDPVRGQVIKATIVLTKDYTPSDSLKNELQDHVKNVTAPYKYPRIIEFVPELPK 542
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh......hhhhhhhhh........hhhhhhhhhhhhhh...eeeeeee....eeeeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh....eeeee........eehhhhhhhh.......hhhhh.....eeeeeee.......eeeeee.hhhhhhhhhhhh........eeee......hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhh...........eeee.....hhhhhhhhhhhhh...eeeee.....eeee.............ee....eeeee............eeeeee...........ee..hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3etc B   3 SLLSQFVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYARDSPEKLAMIWCDDYGNEKIFTFKDLKYYSDKAANFFVKHGIGKGDYVMLTLKSRYDFWYCMLGLHKLGAIAVPATHMLKTRDIVYRIEKAGLKMIVCIAEDDVPEQVDEAHAECGDIPLKKAKVGGDVLEGWIDFRKELEESSPIFERPTGEVSTKNEDICLVYFSSGTAGFPKMVEHDNTYPLGHILTAKYWQNVEDDGLHYTVADSGWGKCVWGKLYGQWIAGCAVFVYDYDRFEAKNMLEKASKYGVTTFCAPPTIYRFLIKEDLSHYNFSTLKYAVVAGEPLNPEVFNRFLEFTGIKLMEGFGQTETVVTIATFPWMEPKPGSIGKPTPGYKIELMDRDGRLCEVGEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHDGYYHTGDMAWMDEDGYLWFVGRADDIIKTSGYKVGPFEVESALIQHPAVLECAITGVPDPVRGQVIKATIVLTKDYTPSDSLKNELQDHVKNVTAPYKYPRIIEFVPELPK 539
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532

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(no "SCOP Domain" information available for 3ETC)

(no "CATH Domain" information available for 3ETC)

(no "Pfam Domain" information available for 3ETC)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8TLW1_METAC | Q8TLW1)

molecular function
	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.
biological process
	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.

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Description

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Ligands, Modified Residues, Ions (7, 21)

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