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Asym./Biol. Unit (Jmol Viewer)

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Title :   ALANINE RACEMASE FROM BACILLUS ANTHRACIS (AMES)

Authors :   R. M. Counago, M. Davlieva, U. Strych, R. E. Hill, K. L. Krause

Date :   30 Apr 09 (Deposition) - 15 Sep 09 (Release) - 15 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   R. M. Counago, M. Davlieva, U. Strych, R. E. Hill, K. L. Krause
Biochemical And Structural Characterization Of Alanine Racemase From Bacillus Anthracis (Ames).
Bmc Struct. Biol. V. 9 53 2009
PubMed-ID: 19695097 | Reference-DOI: 10.1186/1472-6807-9-53
(for further references see the PDB file header)

Molecule 1 - ALANINE RACEMASE
	Chains	:	A, B
	EC Number	:	5.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-TEV-DAL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DAL-1, DAL1
	Organism Common	:	ANTHRAX,ANTHRAX BACTERIUM
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392
	Strain	:	AMES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:270 , TYR A:289 , THR A:316 , MET A:317 , HOH A:404 , HOH A:496 , LLP B:41	BINDING SITE FOR RESIDUE ACT A 398
2	AC2	SOFTWARE	ASN A:131 , ARG A:138	BINDING SITE FOR RESIDUE CL A 399
3	AC3	SOFTWARE	LLP A:41 , TYR A:359 , TYR B:270 , TYR B:289 , THR B:316 , MET B:317 , HOH B:465 , HOH B:535 , HOH B:570	BINDING SITE FOR RESIDUE ACT B 398
4	AC4	SOFTWARE	ASN B:131 , ARG B:138	BINDING SITE FOR RESIDUE CL B 399

(no "SS Bond" information available for 3HA1)

(no "Cis Peptide Bond" information available for 3HA1)

(no "SAP(SNP)/Variant" information available for 3HA1)

(no "PROSITE Motif" information available for 3HA1)

(no "Exon" information available for 3HA1)

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:386
 aligned with Q81VF6_BACAN | Q81VF6 from UniProtKB/TrEMBL  Length:389

    Alignment length:386
                                    13        23        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      
         Q81VF6_BACAN     4 APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPVAKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKSLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLHTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVLVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI 389
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ha1A01     3ha1A02 A:16-229 Alanine racemase                                                                                                                                                                                     -------------------3ha1A01 A:4-15,A:249-389 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeee..hhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhh......eeeehhhhhhhh......eeee............hhhhh.......eeeeeeeeeeeee....eehhhhhee....eeeeee..hhhhh.hhhhh..eeee..eeeeee.......eeeee........eeeeeeee..eeehhhhhhhhh..hhhhhhhh......eeeee..eeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ha1 A   4 APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVkGNAYGHDYVPVAKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKSLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLHTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVLVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI 389
                                    13        23        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      
                                                                41-LLP

Chain B from PDB  Type:PROTEIN  Length:386
 aligned with Q81VF6_BACAN | Q81VF6 from UniProtKB/TrEMBL  Length:389

    Alignment length:386
                                    13        23        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      
         Q81VF6_BACAN     4 APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPVAKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKSLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLHTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVLVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI 389
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ha1B01     3ha1B02 B:16-229 Alanine racemase                                                                                                                                                                                     -------------------3ha1B01 B:4-15,B:249-389 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeee..hhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhh......eeeehhhhhhhh......eeeehhhhhh......hhhhh.......eeeeeeeeeeeee....eehhhhhee....eeeeee..hhhhh.hhhhh..eeee..eeeeee.......eeeee........eeeeeeee..eeehhhhhhhhhh.hhhhhhhh......eeeee..eeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ha1 B   4 APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVkGNAYGHDYVPVAKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKSLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLHTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVLVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI 389
                                    13        23        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      
                                                                41-LLP

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 3HA1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Alanine racemase (53)

Anthrax,anthrax bacterium (Bacillus anthracis) (1)

1a	3ha1A02	A:16-229
1b	3ha1B02	B:16-229

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Homologous Superfamily: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Anthrax,anthrax bacterium (Bacillus anthracis) (1)

2a	3ha1A01	A:4-15,A:249-389
2b	3ha1B01	B:4-15,B:249-389

(no "Pfam Domain" information available for 3HA1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q81VF6_BACAN | Q81VF6)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ha1)

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	3ha1
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	5.1.1.1
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	Q81VF6_BACAN \| Q81VF6	:	2vd8 2vd9

1rcq	ALANINE RACEMASE FROM P.AERUGINOSA
1sft	ALANINE RACEMASE FROM G.STEAROTHERMOPHILUS
1xfc	ALANINE RACEMASE FROM M.TUBERCULOSIS
2vd8	ALANINE RACEMASE FROM B.ANTHRACIS (BA0252)

Description

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Ligands, Modified Residues, Ions (3, 6)

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