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Title :   CRYSTAL STRUCTURE OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE (PPAT) IN COMPLEX WITH ATP FROM ENTEROCOCCUS FAECALIS

Authors :   H. J. Yoon, H. H. Lee, S. W. Suh

Date :   07 Jun 10 (Deposition) - 22 Jun 11 (Release) - 14 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Phosphopantetheine Adenylyltransferase, Ppat, Coenzyme A Biosynthetic Pathway, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. J. Yoon, J. Y. Kang, B. Mikami, H. H. Lee, S. W. Suh
Crystal Structure Of Phosphopantetheine Adenylyltransferase From Enterococcus Faecalis In The Ligand-Unbound State And In Complex With Atp And Pantetheine
Mol. Cells V. 32 431 2011
PubMed-ID: 21912874 | Reference-DOI: 10.1007/S10059-011-0102-Y

Molecule 1 - PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.7.7.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	COAD
	Organism Common	:	STREPTOCOCCUS FAECALIS
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351
	Synonym	:	PPAT, PANTETHEINE-PHOSPHATE ADENYLYLTRANSFERASE, DEPHOSPHO- COA PYROPHOSPHORYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	ATP	6	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:7 , GLY A:17 , HIS A:18 , LEU A:21 , ARG A:89 , GLY A:90 , ARG A:92 , GLU A:100 , ALA A:121 , TYR A:125 , VAL A:128 , SER A:129 , SER A:130 , SER A:131 , HOH A:185 , HOH A:192 , HOH A:200 , HOH A:218 , HOH A:260 , HOH A:304 , HOH A:319	BINDING SITE FOR RESIDUE ATP A 961
2	AC2	SOFTWARE	PHE B:7 , GLY B:9 , SER B:10 , PHE B:11 , GLY B:17 , HIS B:18 , LEU B:21 , ARG B:89 , GLY B:90 , ASP B:96 , GLU B:100 , ALA B:121 , TYR B:125 , VAL B:128 , SER B:129 , SER B:130 , SER B:131 , HOH B:187 , HOH B:190 , HOH B:194 , HOH B:202 , HOH B:209 , HOH B:212 , HOH B:264 , HOH B:344	BINDING SITE FOR RESIDUE ATP B 962
3	AC3	SOFTWARE	PHE C:7 , GLY C:9 , SER C:10 , GLY C:17 , HIS C:18 , LEU C:21 , ARG C:89 , GLY C:90 , GLU C:100 , ALA C:121 , TYR C:125 , VAL C:128 , SER C:129 , SER C:130 , SER C:131 , HOH C:183 , HOH C:185 , HOH C:189 , HOH C:190 , HOH C:215 , HOH C:332 , HOH C:366 , HOH C:413	BINDING SITE FOR RESIDUE ATP C 963
4	AC4	SOFTWARE	PHE D:7 , GLY D:9 , SER D:10 , PHE D:11 , GLY D:17 , HIS D:18 , LEU D:21 , ARG D:89 , GLY D:90 , ARG D:92 , ASP D:96 , GLU D:100 , ALA D:121 , TYR D:125 , VAL D:128 , SER D:129 , SER D:130 , SER D:131 , HOH D:178 , HOH D:193 , HOH D:196 , HOH D:292 , HOH D:309 , HOH D:320 , HOH D:323	BINDING SITE FOR RESIDUE ATP D 964
5	AC5	SOFTWARE	PHE E:7 , GLY E:9 , SER E:10 , GLY E:17 , HIS E:18 , LEU E:21 , ARG E:89 , GLY E:90 , GLU E:100 , ALA E:121 , TYR E:125 , VAL E:128 , SER E:129 , SER E:130 , SER E:131 , HOH E:174 , HOH E:182 , HOH E:206 , HOH E:233	BINDING SITE FOR RESIDUE ATP E 965
6	AC6	SOFTWARE	PHE F:7 , SER F:10 , PHE F:11 , GLY F:17 , HIS F:18 , ARG F:89 , GLY F:90 , GLU F:100 , ALA F:121 , TYR F:125 , VAL F:128 , SER F:129 , SER F:130 , SER F:131 , HOH F:175 , HOH F:190 , HOH F:200 , HOH F:365 , HOH F:392	BINDING SITE FOR RESIDUE ATP F 966

(no "SS Bond" information available for 3ND6)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:12	-	Pro A:13
2	Asp B:12	-	Pro B:13
3	Asp C:12	-	Pro C:13
4	Asp D:12	-	Pro D:13
5	Asp E:12	-	Pro E:13
6	Asp F:12	-	Pro F:13

(no "SAP(SNP)/Variant" information available for 3ND6)

(no "PROSITE Motif" information available for 3ND6)

(no "Exon" information available for 3ND6)

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:152
 aligned with COAD_ENTFA | Q831P9 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           COAD_ENTFA     1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
               SCOP domains d3nd6a_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh...eeeeeeee------..hhhhhhhhhhhhh.....eeeeeee..hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd6 A   1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFI------LFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150        
                                                                38     45

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with COAD_ENTFA | Q831P9 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           COAD_ENTFA     1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
               SCOP domains d3nd6b_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhh....eeeeeeee------..hhhhhhhhhhhhh.....eeeeeee..hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd6 B   1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFI------LFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150        
                                                                38     45

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with COAD_ENTFA | Q831P9 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           COAD_ENTFA     1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
               SCOP domains d3nd6c_ C: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh...eeeeeee.------..hhhhhhhhhhhhh.....eeeeee...hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd6 C   1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFI------LFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150        
                                                                38     45

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with COAD_ENTFA | Q831P9 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           COAD_ENTFA     1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
               SCOP domains d3nd6d_ D: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhh.eeeeee..------..hhhhhhhhhhhhh.....eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhhh...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd6 D   1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFI------LFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150        
                                                                38     45

Chain E from PDB  Type:PROTEIN  Length:152
 aligned with COAD_ENTFA | Q831P9 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           COAD_ENTFA     1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
               SCOP domains d3nd6e_ E: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh...eeeeeeee------..hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd6 E   1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFI------LFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150        
                                                                38     45

Chain F from PDB  Type:PROTEIN  Length:152
 aligned with COAD_ENTFA | Q831P9 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           COAD_ENTFA     1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
               SCOP domains d3nd6f_ F: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----CTP_transf_2-3nd6F01 F:6-136                                                                                                       ---------------------- Pfam domains (1)
           Pfam domains (2) -----CTP_transf_2-3nd6F02 F:6-136                                                                                                       ---------------------- Pfam domains (2)
           Pfam domains (3) -----CTP_transf_2-3nd6F03 F:6-136                                                                                                       ---------------------- Pfam domains (3)
           Pfam domains (4) -----CTP_transf_2-3nd6F04 F:6-136                                                                                                       ---------------------- Pfam domains (4)
           Pfam domains (5) -----CTP_transf_2-3nd6F05 F:6-136                                                                                                       ---------------------- Pfam domains (5)
           Pfam domains (6) -----CTP_transf_2-3nd6F06 F:6-136                                                                                                       ---------------------- Pfam domains (6)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhh.eeeeee..------..hhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd6 F   1 MRKIALFPGSFDPMTNGHLNLIERSAKLFDEVIIGVFI------LFTPEEKKYLIEEATKEMPNVRVIMQETQLTVESAKSLGANFLIRGIRNVKDYEYEKDIAKMNQHLAPEIETVFLLAEEPYAHVSSSLLKEVLRFGGDVSDYLPPNIYHALKQK 158
                                    10        20        30       | -    |   50        60        70        80        90       100       110       120       130       140       150        
                                                                38     45

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Adenine nucleotide alpha hydrolase-like (440)

Superfamily: Nucleotidylyl transferase (325)

Family: automated matches (67)

Protein domain: automated matches (67)

Enterococcus faecalis [TaxId: 1351] (3)

1a	d3nd6a_	A:
1b	d3nd6e_	E:
1c	d3nd6f_	F:
1d	d3nd6b_	B:
1e	d3nd6c_	C:
1f	d3nd6d_	D:

(no "CATH Domain" information available for 3ND6)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HUP (230)

Family: CTP_transf_2 (36)

Enterococcus faecalis (Streptococcus faecalis) (3)

1a	CTP_transf_2-3nd6F01	F:6-136
1b	CTP_transf_2-3nd6F02	F:6-136
1c	CTP_transf_2-3nd6F03	F:6-136
1d	CTP_transf_2-3nd6F04	F:6-136
1e	CTP_transf_2-3nd6F05	F:6-136
1f	CTP_transf_2-3nd6F06	F:6-136

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (COAD_ENTFA | Q831P9)

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: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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004595	pantetheine-phosphate adenylyltransferase activity	Catalysis of the reaction: ATP + pantetheine 4'-phosphate = 3'-dephospho-CoA + diphosphate.
	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:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:12 - Pro A:13	[ RasMol ]
		Asp B:12 - Pro B:13	[ RasMol ]
		Asp C:12 - Pro C:13	[ RasMol ]
		Asp D:12 - Pro D:13	[ RasMol ]
		Asp E:12 - Pro E:13	[ RasMol ]
		Asp F:12 - Pro F:13	[ RasMol ]

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	3nd6
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UniProtKB/Swiss-Prot
	COAD_ENTFA \| Q831P9	:	3nd5 3nd7

3nd5	THE SAME PROTEIN, APO FORM
3nd7	THE SAME PROTEIN COMPLEXED WITH PANTETHEINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 6)

CATH Domains (0, 0)

Pfam Domains (1, 6)

Gene Ontology (9, 9)

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