2JFP - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE

Authors :   T. Lundqvist

Date :   03 Feb 07 (Deposition) - 03 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Glutamate Racemase, Peptidoglycan Biosynthesis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Lundqvist, S. L. Fisher, G. Kern, R. H. A. Folmer, Y. Xue, D. T. Newton, T. A. Keating, R. A. Alm, B. L. M. De Jonge
Exploitation Of Structural And Regulatory Diversity In Glutamate Racemases
Nature V. 447 817 2007
PubMed-ID: 17568739 | Reference-DOI: 10.1038/NATURE05689

Molecule 1 - GLUTAMATE RACEMASE
	Chains	:	A, B
	EC Number	:	5.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	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	CA	2	Ligand/Ion	CALCIUM ION
2	DGL	2	Ligand/Ion	D-GLUTAMIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:44 , THR A:118 , LEU A:119 , PRO A:146 , HOH A:2050 , HOH A:2242	BINDING SITE FOR RESIDUE CA A1271
2	AC2	SOFTWARE	GLY B:44 , THR B:118 , LEU B:119 , HOH B:2068 , HOH B:2261	BINDING SITE FOR RESIDUE CA B1271
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 , VAL A:149 , CYS A:185 , THR A:186 , HIS A:187 , HOH A:2168 , HOH A:2242	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 , VAL B:149 , CYS B:185 , THR B:186 , HIS B:187 , HOH B:2188 , HOH B:2261	BINDING SITE FOR RESIDUE DGL B1270

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

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 2JFP)

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 2JFP)

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:268
 aligned with MURI_ENTFA | Q836J0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261        
           MURI_ENTFA     2 SNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPTIEVTSLDCPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.............eeee..hhhhhhhhhhhhhh......ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jfp A   2 SNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLACPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with MURI_ENTFA | Q836J0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261        
           MURI_ENTFA     2 SNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPTIEVTSLDCPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Asp_Glu_race-2jfpB01 B:7-217                                                                                                                                                                                       ---------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Asp_Glu_race-2jfpB02 B:7-217                                                                                                                                                                                       ---------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhh.............eeee..hhhhhhhhhhhhhh.....eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------ASP_GLU_R-----------------------------------------------------------------------------------------------------ASP_GLU_RAC------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jfp B   2 SNQEAIGLIDSGVGGLTVLKEALKQLPNERLIYLGDTARCPYGPRPAEQVVQFTWEMADFLLKKRIKMLVIACNTATAVALEEIKAALPIPVVGVILPGARAAVKVTKNNKIGVIGTLGTIKSASYEIAIKSKAPAIEVTSLACPKFVPIVESNQYRSSVAKKIVAETLQALQLKGLDTLILGCTHYPLLRPVIQNVMGSHVTLIDSGAETVGEVSMLLDYFDIAHTPEAPTQPHEFYTTGSAKMFEEIASSWLGIENLKAQQIHLGG 269
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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 2JFP)

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

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-2jfpB01	B:7-217
1b	Asp_Glu_race-2jfpB02	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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DGL	[ 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
	2jfp
		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 2vvt

2jfn	CRYSTAL STRUCTURE OF E. COLI GLUTAMATE RACEMASE IN COMPLEX WITH L-GLUTAMATE AND ACTIVATOR UDP-MURNAC-ALA
2jfo	CRYSTAL STRUCTURE OF E. FAECALIS GLUTAMATE RACEMASE IN COMPLEX WITH D- AND L- GLUTAMATE
2jfq	CRYSTAL STRUCTURE OF S. AUREUS GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE
2jfu	CRYSTAL STRUCTURE OF E. FAECIUM GLUTAMATE RACEMASE IN COMPLEX WITH PHOSPHATE

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