1G2W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   E177S MUTANT OF THE PYRIDOXAL-5'-PHOSPHATE ENZYME D-AMINO ACID AMINOTRANSFERASE

Authors :   B. W. Lepore, D. Ringe

Date :   21 Oct 00 (Deposition) - 15 Nov 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Mutant, Pyridoxal-5'-Phosphate, Water Molecule, Internal Aldimine, Aminotransferase, Bacterial Cell Wall Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. W. Van Ophem, B. W. Lepore, K. Kishimoto, D. Ringe, J. M. Manning
Studies On An Active Site Residue, E177, That Affects Binding Of The Coenzyme In D-Amino Acid Transaminase, And Mechanistic Studies On A Suicide Substrate
Biochemistry And Molecular 339 2000 Biology Of Vitamin B6 And Pqq-Dependent Proteins, 10Th Annual International Symposium On Vitamin B6
PubMed: search
(for further references see the PDB file header)

Molecule 1 - D-ALANINE AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PICT113
	Expression System Taxid	:	562
	Expression System Vector	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	D-AMINO ACID AMINOTRANSFERASE

		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	ACT	2	Ligand/Ion	ACETATE ION
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:98 , HIS A:100 , TYR B:31 , PLP B:585	BINDING SITE FOR RESIDUE ACT A 900
2	AC2	SOFTWARE	TYR A:31 , HOH A:739 , ARG B:98 , HIS B:100	BINDING SITE FOR RESIDUE ACT A 901
3	AC3	SOFTWARE	TYR A:31 , HIS A:47 , ARG A:50 , ARG A:138 , LYS A:145 , SER A:179 , SER A:180 , SER A:181 , LEU A:201 , GLY A:203 , ILE A:204 , THR A:205 , SER A:240 , THR A:241 , HOH A:681 , HOH A:712 , HOH A:739	BINDING SITE FOR RESIDUE PLP A 285
4	AC4	SOFTWARE	ACT A:900 , TYR B:31 , HIS B:47 , ARG B:50 , ARG B:138 , SER B:180 , SER B:181 , GLY B:203 , ILE B:204 , THR B:205 , SER B:240 , THR B:241 , LYS B:445 , HOH B:713 , HOH B:738 , HOH B:756	BINDING SITE FOR RESIDUE PLP B 585

(no "SS Bond" information available for 1G2W)

(no "Cis Peptide Bond" information available for 1G2W)

(no "SAP(SNP)/Variant" information available for 1G2W)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_4	PS00770	Aminotransferases class-IV signature.	DAAA_BACYM	178-207	2	A:178-206 B:178-206

(no "Exon" information available for 1G2W)

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:277
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:277
                                    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       271       
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 278
               SCOP domains d1g2wa_ A: D-aminoacid aminotransferase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1g2wA01 A:1-118  [code=3.30.470.10, no name defined]                                                                  1g2wA02 A:119-277 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhh.....hhhhhh..eeeeeeeee..ee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeeeee.................eeeeeeee...hhhhhhhheeeeeee.............hhhhhhhhhhhhh....eeeeee..eeeee...eeeeee..eeee.........hhhhhhhhhhhhhh...ee....hhhhhhh..eeeeee...eeeeeeee..ee......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2w A   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTSGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 277
                                    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       270

Chain B from PDB  Type:PROTEIN  Length:277
 aligned with DAAA_BACYM | P19938 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:277
                                    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       271       
           DAAA_BACYM     2 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTEGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 278
               SCOP domains d1g2wb_ B: D-aminoacid aminotransferase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1g2wB01 B:1-118  [code=3.30.470.10, no name defined]                                                                  1g2wB02 B:119-277 D-amino Acid Aminotransferase, subunit A, domain 2                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.hhh.....hhhhhh..eeeeeeeee..ee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....eeeeeeee.................eeeeeeee...hhhhhhhheeeeeee.............hhhhhhhhhhhhhh...eeeeee..eeeee...eeeeee..eeee.........hhhhhhhhhhhhhh...ee....hhhhhh...eeeeee...eeeeeeee..ee......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_4           ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2w B   1 GYTLWNDQIVKDEEVKIDKEDRGYQFGDGVYEVVKVYNGEMFTVNEHIDRLYASAEKIRITIPYTKDKFHQLLHELVEKNELNTGHIYFQVTRGTSPRAHQFPENTVKPVIIGYTKENPRPLENLEKGVKATFVEDIRWLRCDIKSLNLLGAVLAKQEAHEKGCYEAILHRNNTVTSGSSSNVFGIKDGILYTHPANNMILKGITRDVVIACANEINMPVKEIPFTTHEALKMDELFVTSTTSEITPVIEIDGKLIRDGKVGEWTRKLQKQFETKIP 277
                                    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       270       
                                                                                                                                                                         144||                                                                                                                                   
                                                                                                                                                                          445|                                                                                                                                   
                                                                                                                                                                           146

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 "Pfam Domain" information available for 1G2W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DAAA_BACYM | P19938)

molecular function
	GO:0047810	D-alanine:2-oxoglutarate aminotransferase activity	Catalysis of the reaction: D-alanine + 2-oxoglutarate = pyruvate + D-glutamate.
	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: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.
	GO:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0046437	D-amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of D-amino acids, the D-enantiomers of amino acids.
	GO:0019478	D-amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
	GO:0046416	D-amino acid metabolic process	The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
	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.

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
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLP	[ 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
(no "Cis Peptide Bonds" information available for 1g2w)

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
	1g2w
		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
	DAAA_BACYM \| P19938
		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)
	2.6.1.21
		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
	DAAA_BACYM \| P19938
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	DAAA_BACYM \| P19938	:	1a0g 1daa 2daa 2dab 3daa 3lqs 4daa 5daa

1a0g	1A0G IS THE L201A MUTANT OF THE ENZYME IN THE PYRIDOXAMINE- 5'-PHOSPHATE (PMP) FORM.
1daa	1DAA IS THE WILD TYPE ENZYME IN THE PYRIDOXAMINE-5'- PHOSPHATE (PMP) FORM
2daa	2DAA IS THE WILD-TYPE ENZYME INACTIVATED BY D-CYCLOSERINE
2dab	2DAB IS THE L201A MUTANT OF THE ENZYME IN THE INTERNAL ALDIMINE (PLP) FORM.
3daa	3DAA IS THE WILD-TYPE ENZYME COMPLEXED BY PYRIDOXAL-D- ALANINE
4daa	4DAA IS THE WILD-TYPE ENZYME IN THE INTERNAL ALDIMINE FORM (PLP-FORM_
5daa	5DAA IS THE E177K MUTANT OF THE ENZYME IN THE INTERNAL ALDIMINE (PLP)FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

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