1R43 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF BETA-ALANINE SYNTHASE FROM SACCHAROMYCES KLUYVERI (SELENOMETHIONINE SUBSTITUTED PROTEIN)

Authors :   S. Lundgren, Z. Gojkovic, J. Piskur, D. Dobritzsch

Date :   03 Oct 03 (Deposition) - 11 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Alpha And Beta Protein, One Di-Zinc Center Per Subunit, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Lundgren, Z. Gojkovic, J. Piskur, D. Dobritzsch
Yeast Beta-Alanine Synthase Shares A Structural Scaffold And Origin With Dizinc-Dependent Exopeptidases
J. Biol. Chem. V. 278 51851
PubMed-ID: 14534321 | Reference-DOI: 10.1074/JBC.M308674200
(for further references see the PDB file header)

Molecule 1 - BETA-ALANINE SYNTHASE
	Chains	:	A, B
	EC Number	:	3.5.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P491
	Expression System Strain	:	B843(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYD3
	Organism Scientific	:	LACHANCEA KLUYVERI
	Organism Taxid	:	4934

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 24)

No.	Name	Count	Type	Full Name
1	BIB	2	Ligand/Ion	BETA-AMINO ISOBUTYRATE
2	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:114 , ASP A:125 , GLU A:159 , GLU A:160 , HIS A:226 , ZN A:501 , HOH A:546 , HOH A:559	BINDING SITE FOR RESIDUE ZN A 500
2	AC2	SOFTWARE	ASP A:125 , GLU A:160 , GLN A:229 , HIS A:421 , ZN A:500 , HOH A:559	BINDING SITE FOR RESIDUE ZN A 501
3	AC3	SOFTWARE	HIS B:114 , ASP B:125 , GLU B:159 , HIS B:226 , ZN B:501 , HOH B:1512 , HOH B:1519	BINDING SITE FOR RESIDUE ZN B 500
4	AC4	SOFTWARE	ASP B:125 , GLU B:159 , GLU B:160 , HIS B:421 , ZN B:500 , HOH B:1519	BINDING SITE FOR RESIDUE ZN B 501
5	AC5	SOFTWARE	ARG A:166 , SER A:167 , CYS A:168 , GLN A:401 , BIB A:505	BINDING SITE FOR RESIDUE DTT A 503
6	AC6	SOFTWARE	GLY A:48 , VAL A:49 , ARG A:51 , ASP A:341 , ARG A:342 , LYS A:345 , HOH A:529	BINDING SITE FOR RESIDUE TRS A 504
7	AC7	SOFTWARE	ARG A:322 , ALA A:395 , GLY A:396 , DTT A:503 , HIS B:262 , ASN B:309	BINDING SITE FOR RESIDUE BIB A 505
8	AC8	SOFTWARE	HIS A:262 , ASN A:309 , SER B:167 , TYR B:249 , ARG B:322 , GLY B:396	BINDING SITE FOR RESIDUE BIB B 1505

(no "SS Bond" information available for 1R43)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:304	-	Pro A:305
2	Lys B:304	-	Pro B:305

(no "SAP(SNP)/Variant" information available for 1R43)

(no "PROSITE Motif" information available for 1R43)

(no "Exon" information available for 1R43)

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:438
 aligned with Q96W94_LACKL | Q96W94 from UniProtKB/TrEMBL  Length:455

    Alignment length:438
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447        
         Q96W94_LACKL    18 GTLNLPAAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGMRRLAGTALDGAMRDWFTNECESLGCKVKVDKIGNMFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLMSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLMSSKMIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATMLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSMIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGH 455
               SCOP domains d1r43a1 A:18-247,A:364-455 Peptidase-like beta-alanine synthase, catalytic domain                                                                                                                                                     d1r43a2 A:248-363 Peptidase-like beta-alanine synthase                                                              d1r43a1 A:18-247,A:364-455 Peptidase-like beta-alanine synthase, catalytic domain            SCOP domains
               CATH domains 1r43A01 A:18-247,A:364-455 Zn peptidases                                                                                                                                                                                              1r43A02 A:248-363  [code=3.30.70.360, no name defined]                                                              1r43A01 A:18-247,A:364-455 Zn peptidases                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhh.ee..........ee.....hhhhhhhhhhhhhhhhh...eeee.....eeeee........eeeeee...........hhhhhhhhhhhhhhhhhhh......eeeeee...........hhhhhhhh...hhhhhhh..........hhhhhhhhhh................eeeeee...hhhhhh...eeeeeee.eeeeeeeeee...ee....hhhhh.hhhhhhhhhhhhhhhhhhhh..eee...eeee.....ee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh........eeeeeeeeee..ee.hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhh....eeeeee.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r43 A  18 GTLNLPAAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGmRRLAGTALDGAmRDWFTNECESLGCKVKVDKIGNmFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLmSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLmSSKmIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATmLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSmIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGH 455
                                    27        37        47        57   |    67     |  77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   |   287       297       307       317       327    |  337       347       357       367       377       387       397       407  |    417       427       437       447        
                                                                      61-MSE      73-MSE                 96-MSE                                                                                    187-MSE                                                                                   277-MSE                                                332-MSE                                                                       410-MSE                                         
                                                                                                                                                                                                                                                                                                 281-MSE

Chain B from PDB  Type:PROTEIN  Length:432
 aligned with Q96W94_LACKL | Q96W94 from UniProtKB/TrEMBL  Length:455

    Alignment length:432
                                    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       393       403       413       423       433       443       453  
         Q96W94_LACKL    24 AAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGMRRLAGTALDGAMRDWFTNECESLGCKVKVDKIGNMFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLMSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLMSSKMIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATMLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSMIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGH 455
               SCOP domains d1r43b1 B:24-247,B:364-455 Peptidase-like beta-alanine synthase, catalytic domain                                                                                                                                               d1r43b2 B:248-363 Peptidase-like beta-alanine synthase                                                              d1r43b1 B:24-247,B:364-455 Peptidase-like beta-alanine synthase, catalytic domain            SCOP domains
               CATH domains 1r43B01 B:24-247,B:364-455 Zn peptidases                                                                                                                                                                                        1r43B02 B:248-363  [code=3.30.70.360, no name defined]                                                              1r43B01 B:24-247,B:364-455 Zn peptidases                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhee..........ee.....hhhhhhhhhhhhhhhhh.....ee.....eeeee........eeeee............hhhhhhhhhhhhhhhhhhh......eeeee............hhhhhhhh...hhhhhhhh.........hhhhhhhhhh................eeeeee...hhhhhh...eeee.ee.eeeeeeeeee...ee....hhhhh.hhhhhhhhhhhhhhhhhhhh..eee...eeee.....ee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh........eeeeeeeeee..ee.hhhhhhhhhhhhhhhh....eeee......hhhhhh....eeeeee.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r43 B  24 AAAPLSIASGRLNQTILETGSQFGGVARWGQESHEFGmRRLAGTALDGAmRDWFTNECESLGCKVKVDKIGNmFAVYPGKNGGKPTATGSHLDTQPEAGKYDGILGVLAGLEVLRTFKDNNYVPNYDVCVVVWFNEEGARFARSCTGSSVWSHDLSLEEAYGLmSVGEDKPESVYDSLKNIGYIGDTPASYKENEIDAHFELHIEQGPILEDENKAIGIVTGVQAYNWQKVTVHGVGAHAGTTPWRLRKDALLmSSKmIVAASEIAQRHNGLFTCGIIDAKPYSVNIIPGEVSFTLDFRHPSDDVLATmLKEAAAEFDRLIKINDGGALSYESETLQVSPAVNFHEVCIECVSRSAFAQFKKDQVRQIWSGAGHDSCQTAPHVPTSmIFIPSKDGLSHNYYEYSSPEEIENGFKVLLQAIINYDNYRVIRGH 455
                                    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       393       403      |413       423       433       443       453  
                                                                61-MSE      73-MSE                 96-MSE                                                                                    187-MSE                                                                                   277-MSE                                                332-MSE                                                                       410-MSE                                         
                                                                                                                                                                                                                                                                                           281-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.360, no name defined] (23)

Lachancea kluyveri. Organism_taxid: 4934. (2)

1a	1r43A02	A:248-363
1b	1r43B02	B:248-363

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: Zn peptidases (137)

Lachancea kluyveri. Organism_taxid: 4934. (2)

2a	1r43B01	B:24-247,B:364-455
2b	1r43A01	A:18-247,A:364-455

(no "Pfam Domain" information available for 1R43)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q96W94_LACKL | Q96W94)

molecular function
	GO:0003837	beta-ureidopropionase activity	Catalysis of the reaction: N-carbamoyl-beta-alanine + H2O = beta-alanine + CO2 + NH3.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016813	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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
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		Lys A:304 - Pro A:305	[ RasMol ]
		Lys B:304 - Pro B:305	[ RasMol ]

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	1r43
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	Q96W94_LACKL \| Q96W94	:	1r3n 2v8d 2v8g 2v8h 2v8v 2vl1

1r3n	BETA-ALANINE SYNTHASE FROM SACCHAROMYCES KLUYVERI (NATIVE PROTEIN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 24)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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