3A7A - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI LIPOATE-PROTEIN LIGASE A IN COMPLEX WITH OCTYL-AMP AND APOH-PROTEIN

Authors :   K. Fujiwara, H. Hosaka, A. Nakagawa

Date :   20 Sep 09 (Deposition) - 19 Jan 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Adeniylate-Forming Enzyme, Atp-Binding, Nucleotide-Binding, Transferase, Lipoyl, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Fujiwara, N. Maita, H. Hosaka, K. Okamura-Ikeda, A. Nakagawa, H. Taniguchi
Global Conformational Change Associated With The Two-Step Reaction Catalyzed By Escherichia Coli Lipoate-Protein Ligase A.
J. Biol. Chem. V. 285 9971 2010
PubMed-ID: 20089862 | Reference-DOI: 10.1074/JBC.M109.078717

Molecule 1 - LIPOATE-PROTEIN LIGASE A
	Chains	:	A, C
	EC Number	:	6.3.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LPLA, YJJF, B4386, JW4349
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	LIPOATE-PROTEIN LIGASE

Molecule 2 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-3A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GCVH, B2904, JW2872
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	APOH-PROTEIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	OCT	2	Ligand/Ion	N-OCTANE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	OCT	1	Ligand/Ion	N-OCTANE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	OCT	1	Ligand/Ion	N-OCTANE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:37 , ARG A:70 , GLY A:75 , VAL A:77 , AMP A:402	BINDING SITE FOR RESIDUE OCT A 401
2	AC2	SOFTWARE	GLY A:75 , VAL A:77 , PHE A:78 , ASN A:83 , LYS A:133 , THR A:151 , LEU A:153 , LEU A:165 , VAL A:180 , ARG A:181 , SER A:182 , OCT A:401	BINDING SITE FOR RESIDUE AMP A 402
3	AC3	SOFTWARE	ARG C:70 , GLY C:75 , VAL C:77 , SER C:137 , HIS C:149 , AMP C:402	BINDING SITE FOR RESIDUE OCT C 401
4	AC4	SOFTWARE	GLY C:75 , ALA C:76 , VAL C:77 , PHE C:78 , ASN C:83 , LYS C:133 , THR C:151 , LEU C:153 , LEU C:165 , VAL C:180 , SER C:182 , VAL C:184 , OCT C:401	BINDING SITE FOR RESIDUE AMP C 402

(no "SS Bond" information available for 3A7A)

Asymmetric Unit

No.	Residues
1	Lys A:92	-	Pro A:93
2	Lys C:92	-	Pro C:93

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LPLA_ECOLI_001 *	G	74	S	LPLA_ECOLI	---	---	A/C	G	73	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LPLA_ECOLI_001 *	G	74	S	LPLA_ECOLI	---	---	A	G	73	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LPLA_ECOLI_001 *	G	74	S	LPLA_ECOLI	---	---	C	G	73	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_ECOLI	24-106	2	B:23-105 D:23-105
2	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	LPLA_ECOLI	29-216	2	A:28-215 C:28-215
3	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_ECOLI	49-78	2	B:48-77 D:48-77

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_ECOLI	24-106	1	B:23-105 -
2	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	LPLA_ECOLI	29-216	1	A:28-215 -
3	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_ECOLI	49-78	1	B:48-77 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_ECOLI	24-106	1	- D:23-105
2	BPL_LPL_CATALYTIC	PS51733	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile.	LPLA_ECOLI	29-216	1	- C:28-215
3	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_ECOLI	49-78	1	- D:48-77

(no "Exon" information available for 3A7A)

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:337
 aligned with LPLA_ECOLI | P32099 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           LPLA_ECOLI     2 STLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 338
               SCOP domains d3a7aa1 A:1-246 Two-domain LplA, N-terminal domain                                                                                                                                                                                                    d3a7aa2 A:247-337 Two-domain LplA, C-terminal domain                                        SCOP domains
               CATH domains 3a7aA01 A:1-248 putative lipoate-protein ligase, domain 1                                                                                                                                                                                               ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh.....eeeeee....eeee....hhhhhh.hhhhhhh..eeee.......eee...eeeeeeee.....hhhhhhhhhhhhhhhhh...eee...eeeeee..eeeeeeeeeeee....eeeeeeee...hhhhhhhhh.....eeee....................hhhhhhhhhhhhhhhhh......eee.........hhhhhhhhhh.hhhhh.....eeeeeeeee..eeeeeeeeee..eeeeeeeee....hhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------BPL_LPL_CATALYTIC  PDB: A:28-215 UniProt: 29-216                                                                                                                                            -------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a7a A   1 STLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with GCSH_ECOLI | P0A6T9 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
           GCSH_ECOLI     3 NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 129
               SCOP domains d3a7ab_ B: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 3a7aB00 B:2-128  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeee.....eeeeehhhhhhhhh.eeeee......ee....eeeeeee..eeeeee....eeeeee........hhhhhh.......eeeee..hhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------BIOTINYL_LIPOYL  PDB: B:23-105 UniProt: 24-106                                     ----------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------LIPOYL  PDB: B:48-77          --------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a7a B   2 NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:337
 aligned with LPLA_ECOLI | P32099 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           LPLA_ECOLI     2 STLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 338
               SCOP domains d3a7ac1 C:1-246 Two-domain LplA, N-terminal domain                                                                                                                                                                                                    d3a7ac2 C:247-337 Two-domain LplA, C-terminal domain                                        SCOP domains
               CATH domains 3a7aC01 C:1-248 putative lipoate-protein ligase, domain 1                                                                                                                                                                                               ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh.....eeeeee....eeee....hhhhhh.hhhhhhh..eeee.......eee...eeeeeeeee....hhhhhhhhhhhhhhhh.....ee...eeeee....eeeeeeeeeee...eeeeeeeee...hhhhhhhhhh....eeee...........hhhhh....hhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhhhh.hhhhh.....eeeeeeeee..eeeeeeeeee..eeeeeeeee....hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------BPL_LPL_CATALYTIC  PDB: C:28-215 UniProt: 29-216                                                                                                                                            -------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a7a C   1 STLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR 337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

Chain D from PDB  Type:PROTEIN  Length:127
 aligned with GCSH_ECOLI | P0A6T9 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:127
                                    12        22        32        42        52        62        72        82        92       102       112       122       
           GCSH_ECOLI     3 NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 129
               SCOP domains d3a7ad_ D: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 3a7aD00 D:2-128  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeee.....eeeee..hhhhhhh...eee......ee...eeeeeee....eeeeee...eeeeee........hhhhhh.......eeeee.hhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------BIOTINYL_LIPOYL  PDB: D:23-105 UniProt: 24-106                                     ----------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------------------------LIPOYL  PDB: D:48-77          --------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a7a D   2 NVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

(no "Pfam Domain" information available for 3A7A)

Asymmetric Unit(hide GO term definitions)

Chain A,C (LPLA_ECOLI | P32099)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0016979	lipoate-protein ligase activity	Catalysis of the formation of carbon-nitrogen bonds between lipoate (5-(1,2-dithiolan-3-yl)pentanoate) and a protein.
	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:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0018055	peptidyl-lysine lipoylation	The lipoylation of peptidyl-lysine to form peptidyl-N6-lipoyl-L-lysine.
	GO:0009249	protein lipoylation	The addition of a lipoyl group to an amino acid residue in a protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B,D (GCSH_ECOLI | P0A6T9)

molecular function
	GO:0031405	lipoic acid binding	Interacting selectively and non-covalently with lipoic acid, 1,2-dithiolane-3-pentanoic acid.
biological process
	GO:0019464	glycine decarboxylation via glycine cleavage system	The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005960	glycine cleavage complex	A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.

Asymmetric Unit
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	3a7a
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	GCSH_ECOLI \| P0A6T9
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	LPLA_ECOLI \| P32099
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	6.3.4.-
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UniProtKB/Swiss-Prot
	GCSH_ECOLI \| P0A6T9	:	3a7l 3a8i 3a8j 3a8k 3ab9
	LPLA_ECOLI \| P32099	:	1x2g 1x2h 3a7r 4tvw 4tvy

1x2g	UNLIGANDED LPLA
1x2h	LPLA IN COMPLEX WITH LIPOIC ACID
2e5a	BOVINE LIPOYLTRANSFERASE
3a7l
3a7r

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (12, 14)

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