4BEU - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF VIBRIO CHOLERAE BROAD SPECTRUM RACEMASE

Authors :   C. Carrasco-Lopez, J. A. Hermoso

Date :   12 Mar 13 (Deposition) - 15 Jan 14 (Release) - 09 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

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

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

Reference :   A. Espaillat, C. Carrasco-Lopez, N. Bernardo-Garcia, N. Pietrosemoli, L. H. Otero, L. Alvarez, M. A. De Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso, F. Cava
Structural Basis For The Broad Specificity Of A New Family Of Amino-Acid Racemases.
Acta Crystallogr. , Sect. D V. 70 79 2014
PubMed-ID: 24419381 | Reference-DOI: 10.1107/S1399004713024838

Molecule 1 - ALANINE RACEMASE
	Atcc	:	39315
	Chains	:	A
	EC Number	:	5.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666
	Synonym	:	BROAD SPECTRUM RACEMASE BSRV

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:173 , ASN A:174	BINDING SITE FOR RESIDUE CL A1001
2	AC2	SOFTWARE	LYS A:74 , TYR A:78 , ARG A:173 , HIS A:204 , ASN A:244 , SER A:245 , ARG A:260 , GLY A:262 , GLY A:263 , HOH A:2188 , HOH A:2300 , HOH A:2304 , HOH A:2305 , HOH A:2354 , HOH A:2397	BINDING SITE FOR RESIDUE PLP A1416

Asymmetric Unit

No.	Residues
1	A:70	-	A:96

(no "Cis Peptide Bond" information available for 4BEU)

(no "SAP(SNP)/Variant" information available for 4BEU)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALANINE_RACEMASE	PS00395	Alanine racemase pyridoxal-phosphate attachment site.	ALR2_VIBCH	56-66	1	A:71-81

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALANINE_RACEMASE	PS00395	Alanine racemase pyridoxal-phosphate attachment site.	ALR2_VIBCH	56-66	2	A:71-81

(no "Exon" information available for 4BEU)

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:392
 aligned with ALR2_VIBCH | Q9KSE5 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:392
                                                                                                                                                                                                                                                                                                                                                                                                                         392        
                                    18        28        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       298       308       318       328       338       348       358       368       378       388   |     -  
           ALR2_VIBCH     9 APLHIDTALPDAAQIQQSNSWLEISLGQFQSNIEQFKSHMNANTKICAIMKADAYGNGIRGLMPTIIAQGIPCVGVASNAEARAVRESGFKGELIRVRSASLSEMSSALDLNIEELIGTHQQALDLAELAKQSGKTLKVHIALNDGGMGRNGIDMTTEAGKKEAVSIATQPSLSVVGIMTHFPNYNADEVRAKLAQFKESSTWLMQQANLKREEITLHVANSYTALNVPEAQLDMVRPGGVLFGDLPTNPEYPSIVSFKTRVSSLHHLPKDSTVGYDSTFTTSRDSVLANLPVGYSDGYPRKMGNKAEVLINGQRAKVVGVTSMNTTVVDVTEIKGVLPGQEVVLFGQQQKQSIAVSEMENNAELIFPELYTLWGTSNPRFYVK--------   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh..eeeeeehhhhhhhhhhhhh........eeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhhh....eeee....hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhheeeeehhhhhhhhhhhh..ee...................eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhh...eeee..eeee.........eeee...........eeeee.ee..ee.hhhhhhhhhh.hhhhhhhhhhhhh.eeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------ALANINE_RAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4beu A  24 APLHIDTALPDAAQIQQSNSWLEISLGQFQSNIEQFKSHMNANTKICAIMKADAYGNGIRGLMPTIIAQGIPCVGVASNAEARAVRESGFKGELIRVRSASLSEMSSALDLNIEELIGTHQQALDLAELAKQSGKTLKVHIALNDGGMGRNGIDMTTEAGKKEAVSIATQPSLSVVGIMTHFPNYNADEVRAKLAQFKESSTWLMQQANLKREEITLHVANSYTALNVPEAQLDMVRPGGVLFGDLPTNPEYPSIVSFKTRVSSLHHLPKDSTVGYDSTFTTSRDSVLANLPVGYSDGYPRKMGNKAEVLINGQRAKVVGVTSMNTTVVDVTEIKGVLPGQEVVLFGQQQKQSIAVSEMENNAELIFPELYTLWGTSNPRFYVKSSGHHHHH 415
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413

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 4BEU)

(no "CATH Domain" information available for 4BEU)

(no "Pfam Domain" information available for 4BEU)

Asymmetric Unit(hide GO term definitions)

Chain A (ALR2_VIBCH | Q9KSE5)

molecular function
	GO:0008784	alanine racemase activity	Catalysis of the reaction: L-alanine = D-alanine.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0030632	D-alanine biosynthetic process	The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.
	GO:0006522	alanine metabolic process	The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.
	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.

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
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4beu)

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 \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - 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
	4beu
		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
	ALR2_VIBCH \| Q9KSE5
		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)
	5.1.1.1
		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
	ALR2_VIBCH \| Q9KSE5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ALR2_VIBCH \| Q9KSE5	:	4beq

4be4	CLOSED CONFORMATION OF O. PICEAE STEROL ESTERASE
4be9	OPEN CONFORMATION OF O. PICEAE STEROL ESTERASE
4beq	STRUCTURE OF VIBRIO CHOLERAE BROAD SPECTRUM RACEMASE DOUBLE MUTANT R173A, N174A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

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 (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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