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Title :   EFFECT OF A Y265F MUTANT ON THE TRANSAMINATION BASED CYCLOSERINE INACTIVATION OF ALANINE RACEMASE

Authors :   T. D. Fenn, T. Holyoak, G. F. Stamper, D. Ringe

Date :   12 Oct 04 (Deposition) - 18 Jan 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Alanine Racemase, Cycloserine, Tim Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. D. Fenn, T. Holyoak, G. F. Stamper, D. Ringe
Effect Of A Y265F Mutant On The Transamination-Based Cycloserine Inactivation Of Alanine Racemase
Biochemistry V. 44 5317 2005
PubMed-ID: 15807525 | Reference-DOI: 10.1021/BI047842L

Molecule 1 - ALANINE RACEMASE
	Chains	:	A, B
	EC Number	:	5.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DE3
	Expression System Taxid	:	562
	Gene	:	ALR, DAL
	Mutation	:	YES
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 12)

No.	Name	Count	Type	Full Name
1	4AX	2	Ligand/Ion	(R)-4-AMINO-ISOXAZOLIDIN-3-ONE
2	ACY	2	Ligand/Ion	ACETIC ACID
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
5	PMH	2	Ligand/Ion	(5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
6	PMP	2	Ligand/Ion	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:39 , TYR A:43 , ARG A:136 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:661 , HOH A:670 , HOH A:695 , PHE B:265	BINDING SITE FOR RESIDUE PMP A 501
02	AC2	SOFTWARE	LYS A:39 , TYR A:43 , KCX A:129 , ARG A:136 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:661 , HOH A:670 , HOH A:695 , HOH A:697 , PHE B:265 , TYR B:284 , CYS B:311 , MET B:312 , HOH B:672	BINDING SITE FOR RESIDUE PMH A 503
03	AC3	SOFTWARE	LYS A:39 , TYR A:43 , LEU A:85 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:661 , HOH A:670 , HOH A:695	BINDING SITE FOR RESIDUE PLP A 504
04	AC4	SOFTWARE	LYS A:39 , ARG A:136 , PLP A:504 , HOH A:697 , PHE B:265 , TYR B:284 , CYS B:311 , MET B:312 , HOH B:672	BINDING SITE FOR RESIDUE 4AX B 505
05	AC5	SOFTWARE	VAL B:37 , LYS B:39 , TYR B:43 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:605 , HOH B:643 , HOH B:678	BINDING SITE FOR RESIDUE PMP B 601
06	AC6	SOFTWARE	PHE A:265 , TYR A:284 , CYS A:311 , MET A:312 , HOH A:678 , LYS B:39 , TYR B:43 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:605 , HOH B:628 , HOH B:643 , HOH B:678	BINDING SITE FOR RESIDUE PMH B 603
07	AC7	SOFTWARE	LYS B:39 , TYR B:43 , LEU B:85 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:605 , HOH B:678	BINDING SITE FOR RESIDUE PLP B 604
08	AC8	SOFTWARE	PHE A:265 , TYR A:284 , MET A:312 , HOH A:678 , HOH A:746 , LYS B:39 , ARG B:136 , TYR B:354 , HOH B:628	BINDING SITE FOR RESIDUE 4AX A 605
09	AC9	SOFTWARE	LYS A:39 , ARG A:136 , PHE B:265 , CYS B:311 , MET B:312	BINDING SITE FOR RESIDUE ACY B 502
10	BC1	SOFTWARE	PHE A:265 , CYS A:311 , MET A:312 , LYS B:39 , ARG B:136	BINDING SITE FOR RESIDUE ACY A 602

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:120	-	Pro A:121
2	Gly B:120	-	Pro B:121

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

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.	ALR_GEOSE	36-46	2	A:36-46 B:36-46

(no "Exon" information available for 1XQL)

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:382
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:382
                                    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  
            ALR_GEOSE     2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGR 383
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xqlA01     1xqlA02 A:14-224 Alanine racemase                                                                                                                                                                                  -------------------1xqlA01 A:2-13,A:244-382 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                 - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeeee.hhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhhhh..eeeehhhhhh...hhhhhhhh.......eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhhh.eeee..eeeeee.......eeeee........eeeeeeee..eeehhhhhhhhhh...hhhhhhh.....eeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xql A   2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLkMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSFGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGR 383
                                    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  
                                                                                                                                                         129-KCX

Chain B from PDB  Type:PROTEIN  Length:380
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:380
                                    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
            ALR_GEOSE     2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1xqlB01     1xqlB02 B:14-224 Alanine racemase                                                                                                                                                                                  -------------------1xqlB01 B:2-13,B:244-381 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhh......eeeeehhhhhhh.hhhhhhhhhhhhh..eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeeee.hhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhhhh..eeeehhhhhh...hhhhhhhh.......eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhh..eeee..eeeeee.......eeeee........eeeeeeee..eeehhhhhhhhhh...hhhhhhh.....eeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xql B   2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLkMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSFGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 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
                                                                                                                                                         129-KCX

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 1XQL)

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)

Geobacillus stearothermophilus. Organism_taxid: 1422. (3)

1a	1xqlA02	A:14-224
1b	1xqlB02	B:14-224

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)

Geobacillus stearothermophilus. Organism_taxid: 1422. (3)

2a	1xqlB01	B:2-13,B:244-381
2b	1xqlA01	A:2-13,A:244-382

(no "Pfam Domain" information available for 1XQL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ALR_GEOSE | P10724)

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
		Gly A:120 - Pro A:121	[ RasMol ]
		Gly B:120 - Pro B:121	[ RasMol ]

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	1xql
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	5.1.1.1
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	ALR_GEOSE \| P10724	:	1bd0 1epv 1ftx 1l6f 1l6g 1niu 1sft 1xqk 2sfp 3uw6 4ils

1sft	DETERMINATION OF THE STRUCTURE OF ALANINE RACEMASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.9-A RESOLUTION
1xqk	EFFECT OF A Y265F MUTANT ON THE TRANSAMINATION BASED CYCLOSERINE INACTIVATION OF ALANINE RACEMASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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