2Y28 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SE-MET AMPD DERIVATIVE

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) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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
	Other Details	:	SE-MET DERIVATIVE
	Synonym	:	N-ACETYLMURAMOYL-L-ALANINE AMIDASE, AMPD

		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 (2, 9)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	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:2220	BINDING SITE FOR RESIDUE ZN A1181
2	AC2	SOFTWARE	HIS B:34 , HIS B:154 , ASP B:164 , HOH B:2257	BINDING SITE FOR RESIDUE ZN B1181
3	AC3	SOFTWARE	HIS C:34 , HIS C:154 , ASP C:164 , HOH C:2212	BINDING SITE FOR RESIDUE ZN C1181

(no "SS Bond" information available for 2Y28)

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 2Y28)

(no "PROSITE Motif" information available for 2Y28)

(no "Exon" information available for 2Y28)

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:180
 aligned with AMPD_CITFR | P82974 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           AMPD_CITFR     1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVTP 180
               SCOP domains d2y28a_ A: AmpD protein                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee..ee...ee.....eee.hhhh...eeeeeee.........hhhhhhhh.......hhhhhhhh.......eee.....eee.....eee......ee..ee.hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y28 A   1 mLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNmTGHCNIAPERKTDPGPSFDWARFRALVTP 180
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|      160       170       180
                            |                                                                                                                                                   151-MSE                         
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with AMPD_CITFR | P82974 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
           AMPD_CITFR     1 MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALV 178
               SCOP domains d2y28b_ B: AmpD protein                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee...ee.....eee.hhhh...eeeeeee.........hhhhhhhh.........hhhhh........eee.....eee.....eee......ee..ee.hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y28 B   1 mLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNmTGHCNIAPERKTDPGPSFDWARFRALV 178
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|      160       170        
                            1-MSE                                                                                                                                               151-MSE

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 d2y28c_ C: AmpD protein                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee...ee.....ee.hhhhh...eeeeeee.........hhhhhhhh.......hhhhhhhh.......eee.....eee......ee......ee..ee.hhh.eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y28 C   1 mLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNmTGHCNIAPERKTDPGPSFDWARFRALVT 179
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|      160       170         
                            1-MSE                                                                                                                                               151-MSE

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	d2y28a_	A:
1b	d2y28b_	B:
1c	d2y28c_	C:

(no "CATH Domain" information available for 2Y28)

(no "Pfam Domain" information available for 2Y28)

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
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	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
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	2y28
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	AMPD_CITFR \| P82974
		Comparative Protein Structure Models	:	ModBase
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	3.5.1.28
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		Domain Information	:	XDom
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	AMPD_CITFR \| P82974
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UniProtKB/Swiss-Prot
	AMPD_CITFR \| P82974	:	1j3g 2y2b 2y2c 2y2d 2y2e

1j3g	SOLUTION STRUCTURE OF CITROBACTER FREUNDII AMPD
2y2b	CRYSTAL STRUCTURE OF AMPD IN COMPLEX WITH REACTION PRODUCTS
2y2c	CRYSTAL STRUCTURE OF AMPD APOENZYME
2y2d	CRYSTAL STRUCTURE OF AMPD HOLOENZYME
2y2e	CRYSTAL STRUCTURE OF AMPD GROWN AT PH 5.5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (6, 6)

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