2OHV - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURAL BASIS FOR GLUTAMATE RACEMASE INHIBITION

Authors :   E. E. Kim

Date :   10 Jan 07 (Deposition) - 25 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   K. H. Kim, Y. J. Bong, J. K. Park, K. J. Shin, K. Y. Hwang, E. E. Kim
Structural Basis For Glutamate Racemase Inhibition
J. Mol. Biol. V. 372 434 2007
PubMed-ID: 17658548 | Reference-DOI: 10.1016/J.JMB.2007.05.003
(for further references see the PDB file header)

Molecule 1 - GLUTAMATE RACEMASE
	Chains	:	A
	EC Number	:	5.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MURI
	Organism Scientific	:	STREPTOCOCCUS PYOGENES M1 GAS
	Organism Taxid	:	160490
	Strain	:	ATCC 700294

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NHL	1	Ligand/Ion	(4S)-4-(2-NAPHTHYLMETHYL)-D-GLUTAMIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NHL	2	Ligand/Ion	(4S)-4-(2-NAPHTHYLMETHYL)-D-GLUTAMIC ACID

(no "Site" information available for 2OHV)

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

(no "Cis Peptide Bond" information available for 2OHV)

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_STRP1	179-189	1	A:179-189

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASP_GLU_RACEMASE_2	PS00924	Aspartate and glutamate racemases signature 2.	MURI_STRP1	179-189	2	A:179-189

(no "Exon" information available for 2OHV)

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:258
 aligned with MURI_STRP1 | Q9A1B7 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
           MURI_STRP1     1 MDTRPIGFLDSGVGGLTVVCELIRQLPHEKIVYIGDSARAPYGPRPKKQIKEYTWELVNFLLTQNVKMIVFACNTATAVAWEEVKAALDIPVLGVVLPGASAAIKSTTKGQVGVIGTPMTVASDIYRKKIQLLAPSIQVRSLACPKFVPIVESNEMCSSIAKKIVYDSLAPLVGKIDTLVLGCTHYPLLRPIIQNVMGPSVKLIDSGAECVRDISVLLNYFDINGNYHQKAVEHRFFTTANPEIFQEIASIWLKQKINVEHVTL 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ohvA01 A:1-94,A:207-264  [code=3.40.50.     1860, no name defined]                           2ohvA02 A:95-206  [code=3.40.50.1860, no name defined]                                                          2ohvA01 A:1-94,A:207-26 4                                  CATH domains
               Pfam domains -----Asp_Glu_race-2ohvA01 A:6-215                                                                                                                                                                                      -------------- ---------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhh....eeeee.....-----hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh........-....eeee..hhhhhhhhhhhhh.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_GLU_RAC--------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ohv A   1 MDTRPIGFLDSGVGGLTVVCELIRQLPHEKIVYIGDSARA-----PKKQIKEYTWELVNFLLTQNVKMIVFACNTATAVAWEEVKAALDIPVLGVVLPGASAAIKSTTKGQVGVIGTPMTVASDIYRKKIQLLAPSIQVRSLACPKFVPIVESNEMCSSIAKKIVYDSLAPLVGKIDTLVLGCTHYPLLRPIIQNVMGPSVKLIDSGAECVRDISVLLNYFDINGNYHQ-AVEHRFFTTANPEIFQEIASIWLKQKINVEHVTL 264
                                    10        20        30        40     |  50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        |-|      240       250       260    
                                                                  40    46                                                                                                                                                                                    229 |                                 
                                                                                                                                                                                                                                                                231

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 2OHV)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1860, no name defined] (18)

Streptococcus pyogenes m1 gas. Organism_taxid: 160490. Strain: atcc 700294. (3)

1a	2ohvA02	A:95-206
1b	2ohvA01	A:1-94,A:207-264

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Asp-glut_race (23)

Family: Asp_Glu_race (23)

Streptococcus pyogenes serotype M1 (3)

Asp_Glu_race-2ohvA01

A:6-215

Asymmetric Unit(hide GO term definitions)

Chain A (MURI_STRP1 | Q9A1B7)

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 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
		NHL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 2ohv)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ohv)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 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
	2ohv
		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_STRP1 \| Q9A1B7
		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_STRP1 \| Q9A1B7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MURI_STRP1 \| Q9A1B7	:	2ohg 2oho

1b73	GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS
1zuw	CRYSTAL STRUCTURE OF B.SUBTILIS GLUTAMATE RACEMASE WITH D- GLU
2ohg
2oho

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (1, 1)

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