1YLJ - JenaLib

Title :   ATOMIC RESOLUTION STRUCTURE OF CTX-M-9 BETA-LACTAMASE

Authors :   Y. Chen, J. Delmas, J. Sirot, B. Shoichet, R. Bonnet

Date :   19 Jan 05 (Deposition) - 19 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.98

Chains :   Asym./Biol. Unit : A

Keywords :   Ctx-M, Beta-Lactamase, Anisotropy, Extended-Spectrum, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Chen, J. Delmas, J. Sirot, B. Shoichet, R. Bonnet
Atomic Resolution Structures Of Ctx-M Beta-Lactamases: Extended Spectrum Activities From Increased Mobility And Decreased Stability.
J. Mol. Biol. V. 348 349 2005
PubMed-ID: 15811373 | Reference-DOI: 10.1016/J.JMB.2005.02.010
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:100 , ASP A:101 , ASN A:136 , LYS A:137 , ALA A:140 , THR A:165 , SO4 A:1008 , HOH A:2001 , HOH A:2044 , HOH A:2088 , HOH A:2212 , HOH A:2363 , HOH A:2394 , HOH A:2428 , HOH A:2448 , HOH A:2473	BINDING SITE FOR RESIDUE SUC A 1050
02	AC2	SOFTWARE	ARG A:153 , ARG A:191 , HIS A:197 , HOH A:2081 , HOH A:2103 , HOH A:2151 , HOH A:2342 , HOH A:2365 , HOH A:2421	BINDING SITE FOR RESIDUE SO4 A 1001
03	AC3	SOFTWARE	SER A:70 , SER A:130 , LYS A:234 , THR A:235 , GLY A:236 , SER A:237 , HOH A:2017 , HOH A:2018 , HOH A:2122 , HOH A:2226 , HOH A:2303 , HOH A:2438	BINDING SITE FOR RESIDUE SO4 A 1002
04	AC4	SOFTWARE	ARG A:161 , GLN A:188 , GLN A:192 , HOH A:2037 , HOH A:2076 , HOH A:2138 , HOH A:2155 , HOH A:2210 , HOH A:2225 , HOH A:2324 , HOH A:2375	BINDING SITE FOR RESIDUE SO4 A 1003
05	AC5	SOFTWARE	ARG A:184 , GLN A:188 , HOH A:2012 , HOH A:2106 , HOH A:2180 , HOH A:2219 , HOH A:2225 , HOH A:2248 , HOH A:2374 , HOH A:2432	BINDING SITE FOR RESIDUE SO4 A 1004
06	AC6	SOFTWARE	LYS A:88 , ARG A:178 , THR A:202 , GLN A:203 , HOH A:2063 , HOH A:2128 , HOH A:2397 , HOH A:2479	BINDING SITE FOR RESIDUE SO4 A 1005
07	AC7	SOFTWARE	GLY A:143 , GLY A:144 , PRO A:145 , GLY A:146 , HOH A:2296 , HOH A:2402 , HOH A:2419 , HOH A:2466 , HOH A:2475	BINDING SITE FOR RESIDUE SO4 A 1006
08	AC8	SOFTWARE	SER A:274 , ARG A:276 , ASP A:277 , HOH A:2055 , HOH A:2200 , HOH A:2344	BINDING SITE FOR RESIDUE SO4 A 1007
09	AC9	SOFTWARE	ILE A:108 , LYS A:111 , HIS A:112 , GLU A:288 , SUC A:1050 , HOH A:2056 , HOH A:2071 , HOH A:2119 , HOH A:2240 , HOH A:2270 , HOH A:2377 , HOH A:2473	BINDING SITE FOR RESIDUE SO4 A 1008
10	BC1	SOFTWARE	GLN A:25 , THR A:26 , ASN A:271 , HOH A:2084 , HOH A:2113 , HOH A:2326 , HOH A:2336 , HOH A:2339 , HOH A:2371 , HOH A:2381	BINDING SITE FOR RESIDUE SO4 A 1009
11	BC2	SOFTWARE	ARG A:153 , GLU A:158 , HIS A:197 , HOH A:2080 , HOH A:2091 , HOH A:2227 , HOH A:2337 , HOH A:2342	BINDING SITE FOR RESIDUE SO4 A 1010

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/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:263
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:263
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288   
         Q9L5C8_ECOLX    29 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d1ylja_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1yljA00 A:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------Beta-lactamase2-1yljA01 A:51-263                                                                                                                                                                                  --------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ylj A  25 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9L5C8_ECOLX | Q9L5C8)

molecular function
	GO:0008800	beta-lactamase activity	Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
	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.
biological process
	GO:0030655	beta-lactam antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:166 - Pro A:167	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1ylj
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q9L5C8_ECOLX \| Q9L5C8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.5.2.6
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description