4OX3 - JenaLib

Title :   STRUCTURE OF THE LDCB LD-CARBOXYPEPTIDASE REVEALS THE MOLECULAR BASIS OF PEPTIDOGLYCAN RECOGNITION

Authors :   C. N. Hoyland, C. Aldridge, R. M. Cleverley, K. Sidiq, M. C. Duchene, R. A W. Vollmer, R. J. Lewis

Date :   04 Feb 14 (Deposition) - 11 Jun 14 (Release) - 01 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Las Family, Ld-Carboxypeptidase, Cell Wall Modifying Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. N. Hoyland, C. Aldridge, R. M. Cleverley, M. C. Duchene, G. Minasov, O. Onopriyenko, K. Sidiq, P. J. Stogios, W. F. Anderson, R. A. Daniel, A. Savchenko, W. Vollmer, R. J. Lewis
Structure Of The Ldcb Ld-Carboxypeptidase Reveals The Molecular Basis Of Peptidoglycan Recognition.
Structure V. 22 949 2014
PubMed-ID: 24909784 | Reference-DOI: 10.1016/J.STR.2014.04.015

Compounds

Molecule 1 - PUTATIVE CARBOXYPEPTIDASE YODJ
	Chains	:	A
	EC Number	:	3.4.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 61-273
	Gene	:	BSU19620,YODJ,YODJ,YOKZ
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	224308
	Strain	:	168

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:185 , ASP A:192 , HIS A:244 , PO4 A:302	binding site for residue ZN A 301
2	AC2	SOFTWARE	HIS A:185 , ASP A:192 , GLU A:241 , TRP A:243 , HIS A:244 , ZN A:301 , HOH A:549	binding site for residue PO4 A 302

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhh..eeee..eeee........................ee...........hhhhheehhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee.hhh...hhhhhhhhhhhhhhhhhhhh.eee.....hhhhhh......eeee.hhhhhhhhhhh..hhhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ox3 A  -1 MFSLESQYFNDIKKVDGLETIQNPENILALVNKQYALPGNYEPSDLVIPDVEFSFEEKIQKRYIRKEAADALKTMFDAAKKEGYELAAVSGYRSYDRQKVIFDNEVSLKGERKAKEAVAYPGESEHQTGLAMDISSRSNGFELNEAFGSTADGKWVQDNAYKYGFIIRYPKNKEDITKYEYEPWHLRYVGKKAAKVIQDNDLTLEEYFEKVKKI 273
                            ||      69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
                            ||                                                                                                                                                                                                                    
                           -1|                                                                                                                                                                                                                    
                            61

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
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Still Images

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Databases and Analysis Tools

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	4ox3
		Family and Domain Information	:	ProDom \| SYSTERS
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	3.4.-.-
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Description