2YZN - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D-ALANINE:D-ALANINE LIGASE WITH AMPPNP FROM THERMUS THERMOPHILUS HB8.

Authors :   Y. Kitamuta, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   06 May 07 (Deposition) - 06 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   D-Alanine:D-Alanine Ligase, Cell Shape, Peptidoglycan Synthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of D-Alanine:D-Alanine Ligase With Amppnp From Thermus Thermophilus Hb8
To Be Published
PubMed: search

Molecule 1 - D-ALANINE-D-ALANINE LIGASE
	Chains	:	A, B, C
	EC Number	:	6.3.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ANP	3	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:116 , PHE A:151 , LYS A:153 , SER A:160 , ILE A:163 , GLU A:189 , LYS A:190 , LEU A:192 , GLU A:197 , ASN A:281 , GLU A:282	BINDING SITE FOR RESIDUE ANP A 401
2	AC2	SOFTWARE	LYS B:116 , VAL B:131 , PHE B:151 , LYS B:153 , THR B:157 , GLY B:158 , SER B:159 , SER B:160 , ILE B:163 , GLU B:189 , LYS B:190 , ALA B:191 , LEU B:192 , GLU B:197 , PHE B:272 , ASN B:281 , GLU B:282 , ALA C:220	BINDING SITE FOR RESIDUE ANP B 402
3	AC3	SOFTWARE	ALA B:220 , LYS C:116 , PHE C:151 , LYS C:153 , SER C:159 , SER C:160 , LYS C:190 , ALA C:191 , LEU C:192 , GLU C:197 , ARG C:268 , PHE C:272 , ASN C:281 , GLU C:282 , ASN C:284	BINDING SITE FOR RESIDUE ANP C 403

(no "SS Bond" information available for 2YZN)

Asymmetric Unit

No.	Residues
1	Phe A:65	-	Pro A:66
2	Pro A:148	-	Pro A:149
3	Ser A:193	-	Pro A:194
4	Ile A:238	-	Pro A:239
5	Phe B:65	-	Pro B:66
6	Pro B:148	-	Pro B:149
7	Ser B:193	-	Pro B:194
8	Ile B:238	-	Pro B:239
9	Phe C:65	-	Pro C:66
10	Pro C:148	-	Pro C:149
11	Ser C:193	-	Pro C:194
12	Ile C:238	-	Pro C:239

(no "SAP(SNP)/Variant" information available for 2YZN)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDL_THET8	82-93	3	A:82-93 B:82-93 C:82-93
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDL_THET8	261-288	3	A:261-288 B:261-288 C:261-288

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDL_THET8	82-93	2	A:82-93 B:82-93 -
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDL_THET8	261-288	2	A:261-288 B:261-288 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDL_THET8	82-93	2	- - C:82-93
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDL_THET8	261-288	2	- - C:261-288

(no "Exon" information available for 2YZN)

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:317
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2yzna1 A:1-114 automated matches                                                                                 d2yzna2 A:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeeee........hhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhh......eeeee............eeeee...--....eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....ee...eeeeee..eee...eee..eeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzn A   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANT--SVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    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         
                                                                                                                                                                                      157  |                                                                                                                                                               
                                                                                                                                                                                         160

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2yznb1 B:1-114 automated matches                                                                                 d2yznb2 B:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeee.........hhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee....hhhhhhhhhhh...eeeeee.....eeeeeeee.....eeeeeeeeee....------.....eeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzn B   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPF------YTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    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         
                                                                                                                                                                                                                                                       222    229

Chain C from PDB  Type:PROTEIN  Length:309
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2yznc1 C:1-114 automated matches                                                                                 d2yznc2 C:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Dala_Dala_lig_N-2yznC04 C:1-105                                                                          ----------------Dala_Dala_lig_C-2yznC01 C:122-315                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) Dala_Dala_lig_N-2yznC05 C:1-105                                                                          ----------------Dala_Dala_lig_C-2yznC02 C:122-315                                                                                                                                                                 ---- Pfam domains (2)
           Pfam domains (3) Dala_Dala_lig_N-2yznC06 C:1-105                                                                          ----------------Dala_Dala_lig_C-2yznC03 C:122-315                                                                                                                                                                 ---- Pfam domains (3)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhh.....eeeeee.....eehhhhhhhhhhh..............hhhhh.eeee.........hhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhh.....eeeee............eeeee..........ee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....ee...eeeee...----------..eeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........hhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yzn C   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAP----------GRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|        - |     240       250       260       270       280       290       300       310         
                                                                                                                                                                                                                                                      221        232

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: ATP-grasp (191)

Superfamily: Glutathione synthetase ATP-binding domain-like (158)

Family: automated matches (42)

Protein domain: automated matches (42)

Thermus thermophilus HB8 [TaxId: 300852] (6)

1a	d2yzna2	A:115-319
1b	d2yznb2	B:115-319
1c	d2yznc2	C:115-319

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

Fold: PreATP-grasp domain (131)

Superfamily: PreATP-grasp domain (131)

Family: automated matches (45)

Protein domain: automated matches (45)

Thermus thermophilus HB8 [TaxId: 300852] (3)

2a	d2yzna1	A:1-114
2b	d2yznb1	B:1-114
2c	d2yznc1	C:1-114

(no "CATH Domain" information available for 2YZN)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DDL_THET8 | Q5SHZ3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008716	D-alanine-D-alanine ligase activity	Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
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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	DDL_THET8 \| Q5SHZ3	:	2fb9 2yzg 2yzm 2zdg 2zdh 2zdq

2yzg	RELATED ID: TTK003001114.3 RELATED DB: TARGETDB

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Ligands, Modified Residues, Ions (1, 3)

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