2VVT - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   GLUTAMATE RACEMASE (MURI) FROM E. FAECALIS IN COMPLEX WITH A 9-BENZYL PURINE INHIBITOR

Authors :   B. Geng, G. Breault, J. Comita-Prevoir, R. Petrichko, C. Eyermann, T. Lundqvist, P. Doig, E. Gorseth, B. Noonan

Date :   11 Jun 08 (Deposition) - 24 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A,B

Keywords :   Isomerase, Glutamate Racemase, Peptidoglycan Synthesis, Cell Wall Biogenesis/Degradation, Cell Shape, Benzyl Purine, Muri Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Geng, G. Breault, J. Comita-Prevoir, R. Petrichko, C. Eyermann, T. Lundqvist, P. Doig, E. Gorseth, B. Noonan
Exploring 9-Benzyl Purines As Inhibitors Of Glutamate Racemase (Muri) In Gram-Positive Bacteria.
Bioorg. Med. Chem. Lett. V. 18 4368 2008
PubMed-ID: 18614367 | Reference-DOI: 10.1016/J.BMCL.2008.06.068

Molecule 1 - GLUTAMATE RACEMASE
	Chains	:	A, B
	EC Number	:	5.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-270
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	DGL	2	Ligand/Ion	D-GLUTAMIC ACID
2	I24	2	Ligand/Ion	2-BUTOXY-9-(2,6-DIFLUOROBENZYL)-N-(2-MORPHOLIN-4-YLETHYL)-9H-PURIN-6-AMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:14 , VAL A:152 , GLU A:153 , ASN A:155 , HIS A:187 , LEU A:190 , MET A:246 , ILE A:250 , HOH A:2194 , HOH A:2313 , HOH A:2314	BINDING SITE FOR RESIDUE I24 A1269
2	AC2	SOFTWARE	ASN A:197 , GLY A:200 , SER A:201 , HIS A:202 , HOH A:2235 , VAL B:152 , GLU B:153 , ASN B:155 , GLU B:249 , ILE B:250 , HOH B:2355 , HOH B:2386	BINDING SITE FOR RESIDUE I24 B1269
3	AC3	SOFTWARE	ASP A:11 , SER A:12 , PRO A:42 , TYR A:43 , GLY A:44 , CYS A:74 , ASN A:75 , THR A:76 , THR A:118 , CYS A:185 , THR A:186 , HOH A:2021 , HOH A:2230 , HOH A:2315	BINDING SITE FOR RESIDUE DGL A1270
4	AC4	SOFTWARE	ASP B:11 , SER B:12 , PRO B:42 , TYR B:43 , GLY B:44 , CYS B:74 , ASN B:75 , THR B:76 , THR B:118 , CYS B:185 , THR B:186 , HIS B:187 , HOH B:2282 , HOH B:2388	BINDING SITE FOR RESIDUE DGL B1270

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

Asymmetric/Biological Unit

No.	Residues
1	Cys A:41	-	Pro A:42
2	Cys B:41	-	Pro B:42

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_1	PS00923	Aspartate and glutamate racemases signature 1.	MURI_ENTFA	71-79	2	A:71-79 B:71-79
2	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_ENTFA	181-191	2	A:181-191 B:181-191

(no "Exon" information available for 2VVT)

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:270
 aligned with MURI_ENTFA | Q836J0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:275
                                  1                                                                                                                                                                                                                                                                            
                                  |  4        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       264     
           MURI_ENTFA     - ------MSNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPTIEVTSLDCPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eeeee....hhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh......-----..eeee..hhhhhhhhhhhhhh.....eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvt A  -5 VPRGSHMSNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLACPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTP-----PHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    |    -|      244       254       264     
                                                                                                                                                                                                                                                                    229   235

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with MURI_ENTFA | Q836J0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
           MURI_ENTFA     3 NQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPTIEVTSLDCPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLG 268
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Asp_Glu_race-2vvtB01 B:7-217                                                                                                                                                                                       --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Asp_Glu_race-2vvtB02 B:7-217                                                                                                                                                                                       --------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.............eeee..hhhhhhhhhhhhhh......ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC----------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvt B   3 NQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLACPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLG 268
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

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 '\|'

(no "SCOP Domain" information available for 2VVT)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Asp-glut_race (23)

Family: Asp_Glu_race (23)

Enterococcus faecalis (Streptococcus faecalis) (2)

1a	Asp_Glu_race-2vvtB01	B:7-217
1b	Asp_Glu_race-2vvtB02	B:7-217

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MURI_ENTFA | Q836J0)

molecular function
	GO:0008881	glutamate racemase activity	Catalysis of the reaction: L-glutamate = D-glutamate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0036361	racemase activity, acting on amino acids and derivatives	Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
	GO:0016855	racemase and epimerase activity, acting on amino acids and derivatives	Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.

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
		DGL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		I24	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Cys A:41 - Pro A:42	[ RasMol ]
		Cys B:41 - Pro B:42	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2vvt
		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
	MURI_ENTFA \| Q836J0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	5.1.1.3
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	MURI_ENTFA \| Q836J0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MURI_ENTFA \| Q836J0	:	2jfo 2jfp

2jfo	CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D- AND L-GLUTAMATE
2jfp	CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D- GLUTAMATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File