3HYK - JenaLib

Title :   2.31 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A HOLO-(ACYL-CARRIER-PROTEIN) SYNTHASE FROM BACILLUS ANTHRACIS STR. AMES IN COMPLEX WITH COA (3',5'-ADP)

Authors :   A. S. Halavaty, G. Minasov, T. Skarina, O. Onopriyenko, L. Papazisi, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)

Date :   22 Jun 09 (Deposition) - 30 Jun 09 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

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

Keywords :   Holo-(Acyl-Carrier-Protein) Synthase, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Fatty Acid Biosynthesis, Lipid Synthesis, Magnesium, Metal-Binding, Transferase, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Halavaty, Y. Kim, G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, M. Zhou, O. Onopriyenko, T. Skarina, L. Papazisi, K. Kwon, S. N. Peterson, A. Joachimiak, A. Savchenko, W. F. Anderson
Structural Characterization And Comparison Of Three Acyl-Carrier-Protein Synthases From Pathogenic Bacteria.
Acta Crystallogr. , Sect. D V. 68 1359 2012
PubMed-ID: 22993090 | Reference-DOI: 10.1107/S0907444912029101

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 30)

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	A3P A:124 , HOH A:335 , A3P B:127 , HOH B:336 , HOH B:337 , HOH B:426	BINDING SITE FOR RESIDUE MG B 120
02	AC2	SOFTWARE	HIS A:103 , A3P A:124 , HOH A:331 , HOH A:332 , HOH B:328	BINDING SITE FOR RESIDUE MG A 120
03	AC3	SOFTWARE	A3P A:124 , HOH A:329 , ASP B:8 , GLU B:58 , HOH B:330 , HOH B:334	BINDING SITE FOR RESIDUE MG B 121
04	AC4	SOFTWARE	ILE B:68 , HOH B:212	BINDING SITE FOR RESIDUE CL B 122
05	AC5	SOFTWARE	ASP A:8 , GLU A:58 , HOH A:293 , HOH A:322 , SER C:102 , A3P C:126 , HOH C:303	BINDING SITE FOR RESIDUE MG A 121
06	AC6	SOFTWARE	ILE A:68 , HOH A:277	BINDING SITE FOR RESIDUE CL A 122
07	AC7	SOFTWARE	A3P A:125 , HOH A:296 , HOH A:301 , HOH A:321 , A3P C:126 , HOH C:302	BINDING SITE FOR RESIDUE MG A 123
08	AC8	SOFTWARE	SER B:102 , A3P B:126 , HOH B:312 , ASP C:8 , GLU C:58 , HOH C:290 , HOH C:313	BINDING SITE FOR RESIDUE MG C 120
09	AC9	SOFTWARE	HOH A:282 , HIS C:103 , A3P C:126 , HOH C:323 , HOH C:324	BINDING SITE FOR RESIDUE MG C 121
10	BC1	SOFTWARE	ILE C:68 , HOH C:319	BINDING SITE FOR RESIDUE CL C 122
11	BC2	SOFTWARE	HIS B:103 , A3P B:126 , HOH B:340 , HOH B:341 , HOH C:339	BINDING SITE FOR RESIDUE MG B 123
12	BC3	SOFTWARE	A3P B:126 , HOH B:310 , HOH B:381 , A3P C:125 , HOH C:311 , HOH C:318	BINDING SITE FOR RESIDUE MG C 123
13	BC4	SOFTWARE	GLU B:48 , PHE B:49 , GLY B:52 , ARG B:53 , A3P B:126	BINDING SITE FOR RESIDUE CL B 124
14	BC5	SOFTWARE	ILE C:10 , GLU C:11 , ARG C:14 , HOH C:397 , HOH C:398	BINDING SITE FOR RESIDUE CL C 124
15	BC6	SOFTWARE	SER A:104 , GLU B:11 , ARG B:14 , HOH B:147 , HOH B:333	BINDING SITE FOR RESIDUE CL B 125
16	BC7	SOFTWARE	ARG B:45 , ARG B:53 , ASN B:81 , ARG B:84 , GLY B:85 , LYS B:86 , PRO B:87 , ILE B:101 , SER B:102 , HIS B:103 , MG B:123 , CL B:124 , HOH B:162 , HOH B:228 , HOH B:286 , HOH B:309 , HOH B:310 , HOH B:312 , HOH B:341 , HOH B:381 , ASP C:8 , GLU C:58 , LYS C:62 , GLY C:65 , THR C:66 , GLY C:67 , MG C:120 , MG C:123 , A3P C:125 , HOH C:311 , HOH C:313 , HOH C:339	BINDING SITE FOR RESIDUE A3P B 126
17	BC8	SOFTWARE	LYS B:70 , GLU B:71 , A3P B:126 , HOH B:310 , HOH B:312 , ARG C:14 , MSE C:18 , ARG C:28 , MG C:123 , HOH C:287 , HOH C:288 , HOH C:291 , HOH C:292 , HOH C:304 , HOH C:311 , HOH C:315 , HOH C:316 , HOH C:317 , HOH C:318 , HOH C:339 , HOH C:399	BINDING SITE FOR RESIDUE A3P C 125
18	BC9	SOFTWARE	A3P A:124 , HOH A:329 , ARG B:14 , MSE B:18 , ARG B:28 , ARG B:84 , MG B:120 , HOH B:141 , HOH B:264 , HOH B:328 , HOH B:336 , HOH B:337 , HOH B:342 , HOH B:377 , HOH B:426 , LYS C:70 , GLU C:71 , HOH C:149	BINDING SITE FOR RESIDUE A3P B 127
19	CC1	SOFTWARE	ARG A:45 , ARG A:53 , ASN A:81 , ARG A:84 , GLY A:85 , LYS A:86 , PRO A:87 , ILE A:101 , SER A:102 , HIS A:103 , MG A:120 , HOH A:129 , HOH A:136 , HOH A:138 , HOH A:269 , HOH A:329 , HOH A:331 , HOH A:335 , HOH A:343 , HOH A:424 , ASP B:8 , GLU B:58 , LYS B:62 , GLY B:65 , THR B:66 , GLY B:67 , MG B:120 , MG B:121 , A3P B:127 , HOH B:328 , HOH B:334 , HOH B:336 , HOH B:337	BINDING SITE FOR RESIDUE A3P A 124
20	CC2	SOFTWARE	ASP A:8 , GLU A:58 , LYS A:62 , GLY A:65 , THR A:66 , GLY A:67 , MG A:121 , MG A:123 , A3P A:125 , HOH A:282 , HOH A:296 , HOH A:301 , HOH A:322 , ARG C:45 , ARG C:53 , ASN C:81 , ARG C:84 , GLY C:85 , LYS C:86 , PRO C:87 , ILE C:101 , SER C:102 , HIS C:103 , MG C:121 , HOH C:131 , HOH C:135 , HOH C:302 , HOH C:303 , HOH C:324 , HOH C:325 , HOH C:326 , HOH C:422	BINDING SITE FOR RESIDUE A3P C 126
21	CC3	SOFTWARE	ARG A:14 , ARG A:28 , LYS A:70 , GLU A:71 , MG A:123 , HOH A:194 , HOH A:279 , HOH A:282 , HOH A:283 , HOH A:294 , HOH A:295 , HOH A:296 , HOH A:297 , HOH A:298 , HOH A:301 , HOH A:321 , HOH A:383 , HOH A:388 , HOH A:404 , ARG C:84 , A3P C:126 , HOH C:303	BINDING SITE FOR RESIDUE A3P A 125

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:117
 aligned with ACPS_BACAN | Q81JG3 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:120
                              1                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118
           ACPS_BACAN     - --MIVGIGIDIIELNRIEKMLDGKLKFMERILTENERNVAKGLKGSRLTEFVAGRFAAKEAYSKAVGTGIGKEVSFLDIEVRNDDRGKPILITSTEHIVHLSISHSKEFAVAQVVLESSS 118
               SCOP domains d3hyka_ A: automated m   atches                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeehhhhhhhhh---hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh........hhhhheeee.....eeee.....eeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hyk A  -1 NAmIVGIGIDIIELNRIEKmLD---KFmERILTENERNVAKGLKGSRLTEFVAGRFAAKEAYSKAVGTGIGKEVSFLDIEVRNDDRGKPILITSTEHIVHLSISHSKEFAVAQVVLESSS 118
                              |      8        18 |   | |28        38        48        58        68        78        88        98       108       118
                              |               18-MSE24 |                                                                                            
                              1-MSE             20    26-MSE

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with ACPS_BACAN | Q81JG3 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:118
                             1                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109        
           ACPS_BACAN     - -MIVGIGIDIIELNRIEKMLDGKLKFMERILTENERNVAKGLKGSRLTEFVAGRFAAKEAYSKAVGTGIGKEVSFLDIEVRNDDRGKPILITSTEHIVHLSISHSKEFAVAQVVLESS 117
               SCOP domains d3hykb_ B: automated    matches                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeehhhhhhhh.---hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhheeee.....eeee.....eeeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyk B   0 AmIVGIGIDIIELNRIEKmLD---KFmERILTENERNVAKGLKGSRLTEFVAGRFAAKEAYSKAVGTGIGKEVSFLDIEVRNDDRGKPILITSTEHIVHLSISHSKEFAVAQVVLESS 117
                             |       9        19|   | | 29        39        49        59        69        79        89        99       109        
                             1-MSE           18-MSE24 |                                                                                           
                                               20    26-MSE

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with ACPS_BACAN | Q81JG3 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                             1                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109         
           ACPS_BACAN     - -MIVGIGIDIIELNRIEKMLDGKLKFMERILTENERNVAKGLKGSRLTEFVAGRFAAKEAYSKAVGTGIGKEVSFLDIEVRNDDRGKPILITSTEHIVHLSISHSKEFAVAQVVLESSS 118
               SCOP domains d3hykc_ C: automated    matches                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeehhhhhhhhh---hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........hhhhheeee.....eeee.....eeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyk C   0 AmIVGIGIDIIELNRIEKmLD---KFmERILTENERNVAKGLKGSRLTEFVAGRFAAKEAYSKAVGTGIGKEVSFLDIEVRNDDRGKPILITSTEHIVHLSISHSKEFAVAQVVLESSS 118
                             |       9        19|   | | 29        39        49        59        69        79        89        99       109         
                             1-MSE           18-MSE24 |                                                                                            
                                               20    26-MSE

Legend:		→ Mismatch	(orange background)
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	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 (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (ACPS_BACAN | Q81JG3)

molecular function
	GO:0008897	holo-[acyl-carrier-protein] synthase activity	Catalysis of the reaction: CoA + substrate-serine = adenosine 3',5'-bisphosphate + substrate-serine-4'-phosphopantetheine. The transfer of the 4'-phosphopantetheine (Ppant) co-factor from coenzyme A to the hydroxyl side chain of the serine residue of acyl- or peptidyl-carrier protein (ACP or PCP) to convert them from the apo to the holo form.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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