3UMC - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE L-2-HALOACID DEHALOGENASE PA0810

Authors :   P. Petit, P. W. Y. Chan, A. Savchenko, A. F. Yakunin, E. A. Edwards, E. F. P

Date :   13 Nov 11 (Deposition) - 14 Nov 12 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Haloacid Dehalogenase-Like Hydrolase Protein Superfamily, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. W. Y. Chan, T. K. W. To, P. Petit, C. Tran, M. Waelti, A. Savchenko, A. F. Yakunin, E. A. Edwards, E. F. Pai
Structural Adaptations Of L-2-Haloacid Dehalogenases That Enable Hydrolytic Defluorination
To Be Published
PubMed: search

Molecule 1 - HALOACID DEHALOGENASE
	Chains	:	A, B, C, D
	EC Number	:	3.8.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P15TV-L
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PA0810
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	PAO1
	Synonym	:	L-2-HALOACID DEHALOGENASE PA0810

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 30)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
3	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:7 , VAL A:8 , PHE A:9 , SER A:121 , HOH A:560	BINDING SITE FOR RESIDUE CL A 234
2	AC2	SOFTWARE	VAL B:8 , PHE B:9 , SER B:121 , HOH B:559	BINDING SITE FOR RESIDUE CL B 234
3	AC3	SOFTWARE	ASP C:7 , VAL C:8 , PHE C:9 , SER C:121 , HOH C:278	BINDING SITE FOR RESIDUE CL C 234
4	AC4	SOFTWARE	GLU A:27 , THR A:33 , GLN C:46 , HOH C:456 , HOH C:556 , HOH C:558	BINDING SITE FOR RESIDUE NA C 235
5	AC5	SOFTWARE	ASP D:7 , VAL D:8 , PHE D:9 , SER D:121 , HOH D:476	BINDING SITE FOR RESIDUE CL D 234
6	AC6	SOFTWARE	GLU B:27 , THR B:33 , GLN D:46 , HOH D:457 , HOH D:555 , HOH D:557	BINDING SITE FOR RESIDUE NA D 235

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

Asymmetric Unit

No.	Residues
1	Lys A:152	-	Pro A:153
2	Lys B:152	-	Pro B:153
3	Lys C:152	-	Pro C:153
4	Lys D:152	-	Pro D:153

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

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

(no "Exon" information available for 3UMC)

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
	(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:236
 aligned with Q9I5C9_PSEAE | Q9I5C9 from UniProtKB/TrEMBL  Length:233

    Alignment length:236
                                 1                                                                                                                                                                                                                                      
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
         Q9I5C9_PSEAE     - -----MRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAMDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGMHALKADYWLAALSNGNTALMLDVARHAGLPWDMLLCADLFGHYKPDPQVYLGACRLLDLPPQEVMLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLAA 231
               SCOP domains d3umca_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee......eehhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.ee..hhhhhhhhhh...eeee....hhhhhhhhhhhhh....ee.hhhhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeeee.....................eee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3umc A  -4 LYFQGmRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAmDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGmHALKADYWLAALSNGNTALmLDVARHAGLPWDmLLCADLFGHYKPDPQVYLGACRLLDLPPQEVmLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLAA 231
                                 |   5        15        25        35        45     |  55        65        75        85        95       105  |    115       125  |    135     | 145       155       165       175       185       195       205       215       225      
                                 1-MSE                                            51-MSE                                                  108-MSE             128-MSE      141-MSE                         173-MSE

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with Q9I5C9_PSEAE | Q9I5C9 from UniProtKB/TrEMBL  Length:233

    Alignment length:234
                             1                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
         Q9I5C9_PSEAE     - -MRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAMDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGMHALKADYWLAALSNGNTALMLDVARHAGLPWDMLLCADLFGHYKPDPQVYLGACRLLDLPPQEVMLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLAASA 233
               SCOP domains d3umcb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee......eehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.ee..hhhhhhhhhhhhheeeeee..hhhhhhhhhhhhh....eeeehhhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeeee.....................eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3umc B   0 GmRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAmDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGmHALKADYWLAALSNGNTALmLDVARHAGLPWDmLLCADLFGHYKPDPQVYLGACRLLDLPPQEVmLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLAASA 233
                             |       9        19        29        39        49 |      59        69        79        89        99       109       119       129       139 |     149       159       169   |   179       189       199       209       219       229    
                             1-MSE                                            51-MSE                                                  108-MSE             128-MSE      141-MSE                         173-MSE

Chain C from PDB  Type:PROTEIN  Length:233
 aligned with Q9I5C9_PSEAE | Q9I5C9 from UniProtKB/TrEMBL  Length:233

    Alignment length:233
                             1                                                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229   
         Q9I5C9_PSEAE     - -MRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAMDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGMHALKADYWLAALSNGNTALMLDVARHAGLPWDMLLCADLFGHYKPDPQVYLGACRLLDLPPQEVMLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLAAS 232
               SCOP domains d3umcc_ C: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eehhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.ee..hhhhhhhhhhhhheeeeee..hhhhhhhhhhhhh....eeeehhhhh....hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.....................eee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3umc C   0 GmRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAmDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGmHALKADYWLAALSNGNTALmLDVARHAGLPWDmLLCADLFGHYKPDPQVYLGACRLLDLPPQEVmLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLAAS 232
                             |       9        19        29        39        49 |      59        69        79        89        99       109       119       129       139 |     149       159       169   |   179       189       199       209       219       229   
                             1-MSE                                            51-MSE                                                  108-MSE             128-MSE      141-MSE                         173-MSE

Chain D from PDB  Type:PROTEIN  Length:227
 aligned with Q9I5C9_PSEAE | Q9I5C9 from UniProtKB/TrEMBL  Length:233

    Alignment length:231
                             1                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229 
         Q9I5C9_PSEAE     - -MRAILFDVFGTLVDWRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAMDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGMHALKADYWLAALSNGNTALMLDVARHAGLPWDMLLCADLFGHYKPDPQVYLGACRLLDLPPQEVMLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLA 230
               SCOP domains d3umcd_ D: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eehhhhhhhhhhhhhh.----.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.ee..hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeeehhhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeee......................ee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3umc D   0 GmRAILFDVFGTLVDWRSSLIEQFQALERE----LPCVELTDRWRQQYKPAmDRVRNGQAPWQHLDQLHRQSLEALAGEFGLALDEALLQRITGFWHRLRPWPDTLAGmHALKADYWLAALSNGNTALmLDVARHAGLPWDmLLCADLFGHYKPDPQVYLGACRLLDLPPQEVmLCAAHNYDLKAARALGLKTAFIARPLEYGPGQSQDLAAEQDWDLIASDLLDLHRQLA 230
                             |       9        19        29    |   39        49 |      59        69        79        89        99       109       119       129       139 |     149       159       169   |   179       189       199       209       219       229 
                             1-MSE                      29   34               51-MSE                                                  108-MSE             128-MSE      141-MSE                         173-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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: automated matches (99)

Protein domain: automated matches (99)

Pseudomonas aeruginosa [TaxId: 287] (1)

1a	d3umca_	A:
1b	d3umcb_	B:
1c	d3umcc_	C:
1d	d3umcd_	D:

(no "CATH Domain" information available for 3UMC)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9I5C9_PSEAE | Q9I5C9)

molecular function
	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:0019120	hydrolase activity, acting on acid halide bonds, in C-halide compounds	Catalysis of the hydrolysis of any acid halide bond in substances containing halogen atoms in organic linkage.
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 Unit
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	Cis Peptide Bonds
		Lys A:152 - Pro A:153	[ RasMol ]
		Lys B:152 - Pro B:153	[ RasMol ]
		Lys C:152 - Pro C:153	[ RasMol ]
		Lys D:152 - Pro D:153	[ RasMol ]

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3um9	CRYSTAL STRUCTURE OF THE DEFLUORINATING L-2-HALOACID DEHALOGENASE BPRO0530
3umb	CRYSTAL STRUCTURE OF THE L-2-HALOACID DEHALOGENASE RSC1362
3umg	CRYSTAL STRUCTURE OF THE DEFLUORINATING L-2-HALOACID DEHALOGENASE RHA0230

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