2Y2D - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AMPD HOLOENZYME

Authors :   C. Carrasco-Lopez, A. Rojas-Altuve, W. Zhang, D. Hesek, M. Lee, S. Barb I. Andre, N. Silva-Martin, M. Martinez-Ripoll, S. Mobashery, J. A. He

Date :   14 Dec 10 (Deposition) - 20 Jul 11 (Release) - 14 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Hydrolase, Peptidoglycan Amidase, Amidase_2 Family, Activation Mechanism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Carrasco-Lopez, A. Rojas-Altuve, W. Zhang, D. Hesek, M. Lee, S. Barbe, I. Andre, P. Ferrer, N. Silva-Martin, G. R. Castro, M. Martinez-Ripoll, S. Mobashery, J. A. Hermoso
Crystal Structures Of Bacterial Peptidoglycan Amidase Ampd And An Unprecedented Activation Mechanism.
J. Biol. Chem. V. 286 31714 2011
PubMed-ID: 21775432 | Reference-DOI: 10.1074/JBC.M111.264366

Molecule 1 - 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
	Chains	:	A, B, C
	EC Number	:	3.5.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	CITROBACTER FREUNDII
	Organism Taxid	:	546
	Synonym	:	AMPD, N-ACETYLMURAMOYL-L-ALANINE AMIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:34 , HIS A:154 , ASP A:164 , HOH A:2273	BINDING SITE FOR RESIDUE ZN A1180
2	AC2	SOFTWARE	HIS B:34 , HIS B:154 , ASP B:164 , HOH B:2314	BINDING SITE FOR RESIDUE ZN B1180
3	AC3	SOFTWARE	HIS C:34 , HIS C:154 , ASP C:164 , HOH C:2276	BINDING SITE FOR RESIDUE ZN C1180

(no "SS Bond" information available for 2Y2D)

Asymmetric Unit

No.	Residues
1	Leu A:38	-	Pro A:39
2	Asp A:164	-	Pro A:165
3	Leu B:38	-	Pro B:39
4	Asp B:164	-	Pro B:165
5	Leu C:38	-	Pro C:39
6	Asp C:164	-	Pro C:165

(no "SAP(SNP)/Variant" information available for 2Y2D)

(no "PROSITE Motif" information available for 2Y2D)

(no "Exon" information available for 2Y2D)

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:179
 aligned with AMPD_CITFR | P82974 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           AMPD_CITFR     1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVT 179
               SCOP domains d2y2da_ A: AmpD protein                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee...ee.....ee.hhhhh...eeeeeee.........hhhhhhh.......................eee.....eee......ee......ee..ee.....eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y2d A   1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVT 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with AMPD_CITFR | P82974 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           AMPD_CITFR     1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVT 179
               SCOP domains d2y2db_ B: AmpD protein                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee......ee.hhhh...eeeeeee.........hhhhhhh........hhhhhhhh.......eee.....eee.....ee.......ee..ee.hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y2d B   1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVT 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain C from PDB  Type:PROTEIN  Length:179
 aligned with AMPD_CITFR | P82974 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           AMPD_CITFR     1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVT 179
               SCOP domains d2y2dc_ C: AmpD protein                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee...ee........hhhhh...eeeeeee.........hhhhhhhhh........hhhhhh.......eee.....eee..............ee..ee.hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y2d C   1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVT 179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: N-acetylmuramoyl-L-alanine amidase-like (59)

Superfamily: N-acetylmuramoyl-L-alanine amidase-like (59)

Family: N-acetylmuramoyl-L-alanine amidase-like (53)

Protein domain: AmpD protein (6)

Citrobacter freundii [TaxId: 546] (6)

1a	d2y2da_	A:
1b	d2y2db_	B:
1c	d2y2dc_	C:

(no "CATH Domain" information available for 2Y2D)

(no "Pfam Domain" information available for 2Y2D)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (AMPD_CITFR | P82974)

molecular function
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:164 - Pro A:165	[ RasMol ]
		Asp B:164 - Pro B:165	[ RasMol ]
		Asp C:164 - Pro C:165	[ RasMol ]
		Leu A:38 - Pro A:39	[ RasMol ]
		Leu B:38 - Pro B:39	[ RasMol ]
		Leu C:38 - Pro C:39	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
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Access by PDB/NDB ID
	2y2d
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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Access by UniProt ID/Accession number
	AMPD_CITFR \| P82974
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.5.1.28
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		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	AMPD_CITFR \| P82974
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UniProtKB/Swiss-Prot
	AMPD_CITFR \| P82974	:	1j3g 2y28 2y2b 2y2c 2y2e

1j3g	SOLUTION STRUCTURE OF CITROBACTER FREUNDII AMPD
2y28	CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE
2y2b	CRYSTAL STRUCTURE OF AMPD IN COMPLEX WITH REACTION PRODUCTS
2y2c	CRYSTAL STRUCTURE OF AMPD APOENZYME
2y2e	CRYSTAL STRUCTURE OF AMPD GROWN AT PH 5.5

Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (6, 6)

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