2WKX - JenaLib

Title :   CRYSTAL STRUCTURE OF THE NATIVE E. COLI ZINC AMIDASE AMID

Authors :   S. Petrella, F. Kerff, R. Herman, C. Genereux, A. Pennartz, E. Sauvage, P. Charlier

Date :   18 Jun 09 (Deposition) - 12 Jan 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Outer Membrane, Cell Wall Biogenesis/Degradation, Cell Membrane, Metal-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Kerff, S. Petrella, F. Mercier, E. Sauvage, R. Herman, A. Pennartz, A. Zervosen, A. Luxen, J. M. Frere, B. Joris, P. Charlier
Specific Structural Features Of The N- Acetylmuramoyl-L-Alanine Amidase Amid From Escherichia Coli And Mechanistic Implications For Enzymes Of This Family.
J. Mol. Biol. V. 397 249 2010
PubMed-ID: 20036252 | Reference-DOI: 10.1016/J.JMB.2009.12.038

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:35 , HIS A:151 , ASP A:161 , CL A:302	BINDING SITE FOR RESIDUE ZN A 300
2	AC2	SOFTWARE	ALA A:85 , GLY A:86 , HIS A:151 , ARG A:158	BINDING SITE FOR RESIDUE CL A 301
3	AC3	SOFTWARE	HIS A:151 , LYS A:159 , ASP A:161 , ZN A:300 , HOH A:2091	BINDING SITE FOR RESIDUE CL A 302
4	AC4	SOFTWARE	ALA A:201 , LYS A:215 , PRO A:216 , ASP A:217 , MET A:218 , HOH A:2036 , HOH A:2235 , HOH A:2236	BINDING SITE FOR RESIDUE GOL A 303
5	AC5	SOFTWARE	PRO A:145 , ALA A:172 , GLY A:175 , ILE A:176 , GLY A:177 , LYS A:257 , TYR A:258 , GOL A:305 , HOH A:2238	BINDING SITE FOR RESIDUE GOL A 304
6	AC6	SOFTWARE	GLN A:173 , TRP A:179 , PRO A:180 , ASP A:181 , LYS A:257 , GOL A:304 , HOH A:2238 , HOH A:2239	BINDING SITE FOR RESIDUE GOL A 305
7	AC7	SOFTWARE	VAL A:31 , TRP A:90 , ARG A:91 , ALA A:93 , ARG A:95 , ASN A:147 , ASP A:261 , HOH A:2089	BINDING SITE FOR RESIDUE GOL A 306

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:257
 aligned with AMID_ECOLI | P75820 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:257
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       
           AMID_ECOLI    20 EKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD 276
               SCOP domains d2wkxa2 A:5-179 Probable N-acetylmuramoyl-L-alanine amidase YbjR, N-terminal domain                                                                                            d2wkxa1 A:180-261                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee.............eeeeee...hhhhhhhhhh.......eee.....ee..ee..ee..............ee..ee.hhh.eeeeee....eeee..eeee...hhhhhhhhhhhhhhhhhhhh.hhh.eeehhhhh...........hhhhhhhh......hhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wkx A   5 EKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (AMID_ECOLI | P75820)

molecular function
	GO:0009392	N-acetyl-anhydromuramoyl-L-alanine amidase activity	Catalysis of the reaction: GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-Ala + H2O glcNAc-1,6-anhMurNAc + L-Ala-gamma-D-Glu-DAP-D-Ala.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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.
	GO:0009254	peptidoglycan turnover	The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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