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Title :   THE 1.45 A CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM A PATHOGENIC BACTERIUM, PSEUDOMONAS AERUGINOSA, CONTAINS BOTH INTERNAL AND EXTERNAL ALDIMINE FORMS

Authors :   P. Le Magueres, H. Im, A. Dvorak, U. Strych, M. Benedik, K. L. Krause

Date :   04 Nov 03 (Deposition) - 01 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Alpha-Beta Barrel, Beta-Structure For C-Terminal Domain, Internal/External Aldimine Forms, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Lemagueres, H. Im, A. Dvorak, U. Strych, M. Benedik, K. L. Krause
Crystal Structure At 1. 45 A Resolution Of Alanine Racemase From A Pathogenic Bacterium, Pseudomonas Aeruginosa, Contains Both Internal And External Aldimine Forms.
Biochemistry V. 42 14752 2003
PubMed-ID: 14674749 | Reference-DOI: 10.1021/BI030165V
(for further references see the PDB file header)

Molecule 1 - CATABOLIC ALANINE RACEMASE DADX
	Chains	:	A
	EC Number	:	5.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET26
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	DADX
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	DLY	1	Ligand/Ion	D-LYSINE
2	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	DLY	2	Ligand/Ion	D-LYSINE
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:31 , LYS A:33 , TYR A:37 , KCX A:122 , ARG A:129 , HIS A:158 , ASN A:192 , SER A:193 , PRO A:194 , ARG A:208 , GLY A:210 , ILE A:211 , TYR A:341 , DLY A:359 , HOH A:531 , HOH A:603	BINDING SITE FOR RESIDUE PLP A 358
2	AC2	SOFTWARE	LYS A:33 , TYR A:37 , ARG A:129 , TYR A:253 , TYR A:272 , SER A:300 , MET A:301 , ASP A:302 , MET A:303 , TYR A:341 , PLP A:358 , HOH A:518 , HOH A:601 , HOH A:603	BINDING SITE FOR RESIDUE DLY A 359

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

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

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

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_PSEAE	30-40	1	A:30-40

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_PSEAE	30-40	2	A:30-40

(no "Exon" information available for 1RCQ)

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
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Chain A from PDB  Type:PROTEIN  Length:357
 aligned with ALR2_PSEAE | Q9HTQ2 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:357
                                    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       280       290       300       310       320       330       340       350       
           ALR2_PSEAE     1 MRPARALIDLQALRHNYRLAREATGARALAVIKADAYGHGAVRCAEALAAEADGFAVACIEEGLELREAGIRQPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERASLARPLNVWLKMDSGMHRVGFFPEDFSAAHERLRASGKVAKIVMMSHFSRADELDCPRTEEQLAAFAAASQGLEGEISLRNSPAVLGWPKVPSDWVRPGILLYGATPFERAHPLADRLRPVMTLESKVISVRDLPAGEPVGYGARYSTERSQRIGVVAMGYADGYPRHAADGTLVFIDGKPGRLVGRVSMDMLTVDLTDHPQAGLGSRVELWGPNVPVGALAAQFGSIPYQLLCNLKRVPRVYSGA 357
               SCOP domains d1rcqa1d1rcqa2 A:8-233 Alanine racemase                                                                                                                                                                                                  d1rcqa1 A:1-7,A:234-357 Alanine racemase                                                                                     SCOP domains
               CATH domains 1rcqA01  1rcqA02 A:10-216 Alanine racemase                                                                                                                                                                              1rcqA01 A:1-9,A:217-357 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                     CATH domains
               Pfam domains -------Ala_racemase_N-1rcqA01 A:8-218                                                                                                                                                                                     -------------Ala_racemase_C-1rcqA02 A:232-355                                                                                            -- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhh.eeeeehhhhhhh.hhhhhhhhhh....eeee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh.eeeee.hhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhhhhhh.....ee..hhhhhhhh......ee..hhhhhh.........hhhhh...eeeeeeeeeeeee....eehhhhhee....eeeeee..hhhhh.........eeee..eeee.........eeee...........eeeee....hhhhhhhhh..hhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------ALANINE_RAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rcq A   1 MRPARALIDLQALRHNYRLAREATGARALAVIKADAYGHGAVRCAEALAAEADGFAVACIEEGLELREAGIRQPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERASLARPLNVWLkMDSGMHRVGFFPEDFRAAHERLRASGKVAKIVMMSHFSRADELDCPRTEEQLAAFSAASQGLEGEISLRNSPAVLGWPKVPSDWVRPGILLYGATPFERAHPLADRLRPVMTLESKVISVRDLPAGEPVGYGARYSTERRQRIGVVAMGYADGYPRHAADGTLVFIDGKPGRLVGRVSMDMLTVDLTDHPQAGLGSRVELWGPNVPVGALAAQFGSIPYQLLCNLKRVPRVYSGA 357
                                    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       280       290       300       310       320       330       340       350       
                                                                                                                                                   122-KCX

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Ala_racemase_N (19)

Pseudomonas aeruginosa (1)

Ala_racemase_N-1rcqA01

A:8-218

Clan: no clan defined [family: Ala_racemase_C] (18)

Family: Ala_racemase_C (18)

Pseudomonas aeruginosa (1)

Ala_racemase_C-1rcqA02

A:232-355

Asymmetric Unit(hide GO term definitions)

Chain A (ALR2_PSEAE | Q9HTQ2)

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:0006522	alanine metabolic process	The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.

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1bdo	ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE
1epv	ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM D- CYCLOSERINE
1l6f	ALANINE RACEMASE BOUND WITH N-(5'-PHOSPHOPYRIDOXYL)-L- ALANINE
1sft	ALANINE RACEMASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH ACETATE
2sfp	ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR

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