3L8C - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF PROBABLE D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT-1 FROM STREPTOCOCCUS PYOGENES

Authors :   U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   30 Dec 09 (Deposition) - 19 Jan 10 (Release) - 19 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.41

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

Keywords :   Structural Genomics, D-Alanine-Poly(Phosphoribitol) Ligase, Dlta, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo
Structure Of Probable D-Alanine--Poly(Phosphoribitol) Ligase Subunit-1 From Streptococcus Pyogenes
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 1
	Chains	:	A, B
	EC Number	:	6.1.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX4(BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DLTA, M6_SPY1043
	Organism Scientific	:	STREPTOCOCCUS PYOGENES SEROTYPE M6
	Organism Taxid	:	301450
	Synonym	:	D-ALANINE-ACTIVATING ENZYME, DAE, D-ALANINE-D- ALANYL CARRIER PROTEIN LIGASE, DCL

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3L8C)

(no "Site" information available for 3L8C)

(no "SS Bond" information available for 3L8C)

(no "Cis Peptide Bond" information available for 3L8C)

(no "SAP(SNP)/Variant" information available for 3L8C)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMP_BINDING	PS00455	Putative AMP-binding domain signature.	DLTA_STRP6	149-160	2	A:145-156 B:145-156

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMP_BINDING	PS00455	Putative AMP-binding domain signature.	DLTA_STRP6	149-160	1	A:145-156 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMP_BINDING	PS00455	Putative AMP-binding domain signature.	DLTA_STRP6	149-160	1	- B:145-156

(no "Exon" information available for 3L8C)

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:499
 aligned with DLTA_STRP6 | Q5XBN5 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:510
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510
           DLTA_STRP6     1 MIKDMIDSIEQFAQTQADFPVYDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFGAQTYDMLATFVALTKSGHAYIPVDVHSAPERILAIIEIAKPSLIIAIEEFPLTIEGISLVSLSEIESAKLAEMPYERTHSVKGDDNYYIIFTSGTTGQPKGVQISHDNLLSFTNWMIEDAAFDVPKQPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKELVADFKQLFTTIAQLPVGIWTSTPSFADMAMLSDDFCQAKMPALTHFYFDGEELTVSTARKLFERFPSAKIINAYGPTEATVALSAIEITREMVDNYTRLPIGYPKPDSPTYIIDEDGKELSSGEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNILLYGGRLDFQIKYAGYRIELEDVSQQLNQSPMVASAVAVPRYNKEHKVQNLLAYIVVKDGVKERFDRELELTKAIKASVKDHMMSYMMPSKFLYRDSLPLTPNGKIDIKTLINEVN 510
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...eeee...........eeeehhhhhhhhhhh.............eeeeee..---....eeeeehhhhhhhhhhhhhh.........eee......hhhhhhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhh...eeeehhhhhhhhhh.............eeee.....hhhhhhhhhhhh...eeeeee.hhhhh...eeeeehhhhhhhh...eeeee.....eeee............eeeeee..........hhhhhhhheeee..eeeeeeeeeeee.....eeeeee.hhh..-----.hhhhhhhhhhh...eeeeeee........---.eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l8c A  -3 SLKDMIDSIEQFAQTQADFPVYDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFGAQTYDMLATFVALTKSGHAYIPVDVHSAPERILAIIEIAKPSLIIAIEEFPLTIEGISLVSLSEIESAKLAEMPYERTHSVKGDDNYYIIFTS---GQPKGVQISHDNLLSFTNWMIEDAAFDVPKQPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKELVADFKQLFTTIAQLPVGIWTSTPSFADMAMLSDDFCQAKMPALTHFYFDGEELTVSTARKLFERFPSAKIINAYGPTEATVALSAIEITREMVDNYTRLPIGYPKPDSPTYIIDEDGKELSSGEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNILLYGGRLDFQIK-----IELEDVSQQLNQSPMVASAVAVPRYNKEHK---LLAYIVVKDGVKERFDRELELTKAIKASVKDHMMSYMMPSKFLYRDSLPLTPNGKIDIKTLINEVN 506
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146  |   |156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396     |   - |     416       426       436|   |  446       456       466       476       486       496       506
                                                                                                                                                                                  149 153                                                                                                                                                                                                                                                      402   408                          437 441

Chain B from PDB  Type:PROTEIN  Length:510
 aligned with DLTA_STRP6 | Q5XBN5 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:510
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510
           DLTA_STRP6     1 MIKDMIDSIEQFAQTQADFPVYDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFGAQTYDMLATFVALTKSGHAYIPVDVHSAPERILAIIEIAKPSLIIAIEEFPLTIEGISLVSLSEIESAKLAEMPYERTHSVKGDDNYYIIFTSGTTGQPKGVQISHDNLLSFTNWMIEDAAFDVPKQPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKELVADFKQLFTTIAQLPVGIWTSTPSFADMAMLSDDFCQAKMPALTHFYFDGEELTVSTARKLFERFPSAKIINAYGPTEATVALSAIEITREMVDNYTRLPIGYPKPDSPTYIIDEDGKELSSGEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNILLYGGRLDFQIKYAGYRIELEDVSQQLNQSPMVASAVAVPRYNKEHKVQNLLAYIVVKDGVKERFDRELELTKAIKASVKDHMMSYMMPSKFLYRDSLPLTPNGKIDIKTLINEVN 510
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------AMP-binding-3l8cB01 B:26-428                                                                                                                                                                                                                                                                                                                                                                                       ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------AMP-binding-3l8cB02 B:26-428                                                                                                                                                                                                                                                                                                                                                                                       ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh..eeee............eeehhhhhhhhhh..............eeeeee.........eeeeehhhhhhhhhhhhhh.........eee......hhhhhhhhhhhhhhh.eeee.......hhhhhhhhhh.....eeeehhhhhhhhh..............eeee.....hhhhhhhhhhhh...eeeeee.hhhhh...eeeeehhhhhhhh......ee.....eeee............eeeeee..........hhhhhhhheeee..eeeeeeeeeeee.....eeeeee...eeee..eeeehhhhhhhhh....eeeeeeeeee.....eeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhhh.......eeee............hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l8c B  -3 SLKDMIDSIEQFAQTQADFPVYDCLGERRTYGQLKRDSDSIAAFIDSLALLAKSPVLVFGAQTYDMLATFVALTKSGHAYIPVDVHSAPERILAIIEIAKPSLIIAIEEFPLTIEGISLVSLSEIESAKLAEMPYERTHSVKGDDNYYIIFTSGTTGQPKGVQISHDNLLSFTNWMIEDAAFDVPKQPQMLAQPPYSFDLSVMYWAPTLALGGTLFALPKELVADFKQLFTTIAQLPVGIWTSTPSFADMAMLSDDFCQAKMPALTHFYFDGEELTVSTARKLFERFPSAKIINAYGPTEATVALSAIEITREMVDNYTRLPIGYPKPDSPTYIIDEDGKELSSGEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNILLYGGRLDFQIKYAGYRIELEDVSQQLNQSPMVASAVAVPRYNKEHKVQNLLAYIVVKDGVKERFDRELELTKAIKASVKDHMMSYMMPSKFLYRDSLPLTPNGKIDIKTLINEVN 506
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506

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 '\|'

(no "SCOP Domain" information available for 3L8C)

(no "CATH Domain" information available for 3L8C)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ANL (32)

Family: AMP-binding (32)

Streptococcus pyogenes serotype M6 (1)

1a	AMP-binding-3l8cB01	B:26-428
1b	AMP-binding-3l8cB02	B:26-428

Asymmetric Unit(hide GO term definitions)

Chain A,B (DLTA_STRP6 | Q5XBN5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0047473	D-alanine-poly(phosphoribitol) ligase activity	Catalysis of the reaction: poly(ribitol phosphate) + D-alanine + ATP = O-D-alanyl-poly(ribitol phosphate) + diphosphate + AMP.
	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:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
	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:0070395	lipoteichoic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of lipoteichoic acid, which is a major component of the cell wall of gram-positive bacteria and typically consists of a chain of glycerol-phosphate repeating units linked to a glycolipid anchor.
	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.
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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Biological Units
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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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