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Title :   THE 2.15 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS ALANINE RACEMASE

Authors :   E. R. Scaletti, S. R. Luckner, K. L. Krause

Date :   04 Oct 11 (Deposition) - 28 Dec 11 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Isomerase, Plp-Dependent Enzymes (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. R. Scaletti, S. R. Luckner, K. L. Krause
Structural Features And Kinetic Characterization Of Alanine Racemase From Staphylococcus Aureus (Mu50)
Acta Crystallogr. , Sect. D V. 68 82 2012
PubMed-ID: 22194336 | Reference-DOI: 10.1107/S0907444911050682

Molecule 1 - ALANINE RACEMASE 1
	Chains	:	A, B
	EC Number	:	5.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector	:	PET26B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	MU50

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 17)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	13	Ligand/Ion	SULFATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:39 , TYR A:43 , HIS A:168 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:2032	BINDING SITE FOR RESIDUE PLP A1039
02	AC2	SOFTWARE	TYR A:228 , GLN A:234 , HIS A:240 , LEU A:241 , ARG A:336 , HOH A:2118	BINDING SITE FOR RESIDUE SO4 A1383
03	AC3	SOFTWARE	SER A:107 , LYS A:108 , GLN A:109 , THR A:146	BINDING SITE FOR RESIDUE SO4 A1384
04	AC4	SOFTWARE	VAL A:48 , LYS A:49 , ARG A:52 , HIS A:76	BINDING SITE FOR RESIDUE SO4 A1385
05	AC5	SOFTWARE	HIS A:335 , ARG A:336 , GLU A:337 , HOH A:2138	BINDING SITE FOR RESIDUE SO4 A1386
06	AC6	SOFTWARE	HIS A:29 , PRO A:30 , ASN A:31 , LYS A:32	BINDING SITE FOR RESIDUE SO4 A1387
07	AC7	SOFTWARE	LYS A:131 , ARG A:138 , LEU A:139 , HIS A:168 , HOH A:2080 , GLN B:314	BINDING SITE FOR RESIDUE SO4 A1388
08	AC8	SOFTWARE	CYS A:311 , MET A:312 , HOH A:2135 , LYS B:39 , PLP B:1039	BINDING SITE FOR RESIDUE ACT A1389
09	AC9	SOFTWARE	ACT A:1389 , LYS B:39 , TYR B:43 , HIS B:168 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:2015	BINDING SITE FOR RESIDUE PLP B1039
10	BC1	SOFTWARE	TYR B:228 , GLN B:234 , HIS B:240 , LEU B:241 , ARG B:336 , HOH B:2067 , HOH B:2076	BINDING SITE FOR RESIDUE SO4 B1383
11	BC2	SOFTWARE	LYS B:49 , ARG B:52 , HIS B:76	BINDING SITE FOR RESIDUE SO4 B1384
12	BC3	SOFTWARE	SER A:361 , ARG A:362 , HOH A:2152 , LEU B:360 , SER B:361 , ARG B:362 , HOH B:2105	BINDING SITE FOR RESIDUE SO4 B1385
13	BC4	SOFTWARE	SER B:107 , LYS B:108 , GLN B:109	BINDING SITE FOR RESIDUE SO4 B1386
14	BC5	SOFTWARE	HIS B:335 , ARG B:336 , GLU B:337 , HOH B:2096	BINDING SITE FOR RESIDUE SO4 B1387
15	BC6	SOFTWARE	LYS A:108 , LYS A:112 , HIS B:29 , PRO B:30 , ASN B:31 , LYS B:32 , ASP B:211 , GLN B:213	BINDING SITE FOR RESIDUE SO4 B1388
16	BC7	SOFTWARE	LYS B:131 , ARG B:138 , LEU B:139 , HIS B:168	BINDING SITE FOR RESIDUE SO4 B1389
17	BC8	SOFTWARE	LYS A:39 , TYR A:354 , TYR B:284 , CYS B:311 , MET B:312 , HOH B:2078 , HOH B:2091	BINDING SITE FOR RESIDUE ACT B1390

(no "SS Bond" information available for 4A3Q)

(no "Cis Peptide Bond" information available for 4A3Q)

(no "SAP(SNP)/Variant" information available for 4A3Q)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALANINE_RACEMASE	PS00395	Alanine racemase pyridoxal-phosphate attachment site.	ALR1_STAAM	36-46	2	A:36-46 B:36-46

(no "Exon" information available for 4A3Q)

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:356
 aligned with ALR1_STAAM | P63479 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:381
                                    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       281       291       301       311       321       331       341       351       361       371       381 
           ALR1_STAAM     2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTNTYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTLQAGESVSYGATYTATDPTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhhhhhhhhhh....ee.ee.........hhhhhhhhhhh...eeee..hhhhhhhhh.....eeee........hhhhhhh.eeeee..hhhhhhhhhh........eeeeee............hhhhhhhhhhhhh...eeeeeee...-------hhhhhhhhhhhhhhh......eeeee.hhhhhh.......ee............hhhhhh........eeeeeee.eee.------------------.eeeee..............eeeee..eeeee........eeeee.......eeeeee.........hhhhhhhh...hhhhhhh......eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a3q A   2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTNTYQEVIEIIQQYEQLVFEGVFTHF-------DMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKT------------------TTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       | -     | 181       191       201       211       221       231       241       251    |    -         -   |   281       291       301       311       321       331       341       351       361       371       381 
                                                                                                                                                                                                 169     177                                                                            256                275

Chain B from PDB  Type:PROTEIN  Length:356
 aligned with ALR1_STAAM | P63479 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:381
                                    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       281       291       301       311       321       331       341       351       361       371       381 
           ALR1_STAAM     2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTNTYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTLQAGESVSYGATYTATDPTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhhhhhhhhhh....ee.ee.........hhhhhhhhhh....eeee..hhhhhhhhhh....eeee........hhhhhhh...eee..hhhhhhhhhh........eeeeee............hhhhhhhhhhhhh...eeeeeee...---------hhhhhhhhhhhhh......eee...hhhhhh.......ee............hhhhhh........eeeeeee.eeee.----------------..eeeee..............eeeee..eeeee........eeee........eeeeee.........hhhhhhhh...hhhhhhh......eeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a3q B   2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTNTYQEVIEIIQQYEQLVFEGVFTHF---------TTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTL----------------PTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       | -       181       191       201       211       221       231       241       251     |   -         -  |    281       291       301       311       321       331       341       351       361       371       381 
                                                                                                                                                                                                 169       179                                                                           257              274

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 4A3Q)

(no "CATH Domain" information available for 4A3Q)

(no "Pfam Domain" information available for 4A3Q)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ALR1_STAAM | P63479)

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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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