3D3S - JenaLib

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Title :   CRYSTAL STRUCTURE OF L-2,4-DIAMINOBUTYRIC ACID ACETYLTRANSFERASE FROM BORDETELLA PARAPERTUSSIS

Authors :   Y. Kim, L. Volkart, R. Jedrzejczak, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)

Date :   12 May 08 (Deposition) - 15 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

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

Keywords :   Alpha-Beta-Alpha Sandwich, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Acyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, L. Volkart, R. Jedrzejczak, A. Joachimiak
Crystal Structure Of L-2, 4-Diaminobutyric Acid Acetyltransferase From Bordetella Parapertussis.
To Be Published
PubMed: search

Molecule 1 - L-2,4-DIAMINOBUTYRIC ACID ACETYLTRANSFERASE
	Atcc	:	BAA-587
	Chains	:	A, B, C, D
	EC Number	:	2.3.1.178
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P11
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	ECTA, BPP1888
	Organism Scientific	:	BORDETELLA PARAPERTUSSIS 12822
	Organism Taxid	:	257311
	Strain	:	12822 / NCTC 13253
	Synonym	:	DABA ACETYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 26)

No.	Name	Count	Type	Full Name
1	DAB	2	Ligand/Ion	2,4-DIAMINOBUTYRIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	DAB	-1	Ligand/Ion	2,4-DIAMINOBUTYRIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 12)

No.	Name	Count	Type	Full Name
1	DAB	2	Ligand/Ion	2,4-DIAMINOBUTYRIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG B:85 , LEU B:86 , GLY B:87 , ARG B:88 , THR B:120	BINDING SITE FOR RESIDUE SO4 B 165
02	AC2	SOFTWARE	ARG B:82 , GLY B:83 , HIS B:84 , ARG B:85	BINDING SITE FOR RESIDUE SO4 B 166
03	AC3	SOFTWARE	SER A:49 , PRO A:50 , GLY A:51 , ARG A:53	BINDING SITE FOR RESIDUE SO4 A 165
04	AC4	SOFTWARE	ARG B:1 , SER B:49 , PRO B:50 , GLY B:51 , ARG B:53	BINDING SITE FOR RESIDUE SO4 B 167
05	AC5	SOFTWARE	SER C:49 , PRO C:50 , GLY C:51 , ARG C:53	BINDING SITE FOR RESIDUE SO4 C 165
06	AC6	SOFTWARE	ARG D:1 , SER D:49 , PRO D:50 , GLY D:51 , ARG D:53	BINDING SITE FOR RESIDUE SO4 D 165
07	AC7	SOFTWARE	ARG D:85 , LEU D:86 , GLY D:87 , ARG D:88 , THR D:120	BINDING SITE FOR RESIDUE SO4 D 166
08	AC8	SOFTWARE	ARG A:119	BINDING SITE FOR RESIDUE SO4 A 166
09	AC9	SOFTWARE	ARG A:82 , GLY A:83 , HIS A:84 , ARG A:85	BINDING SITE FOR RESIDUE SO4 A 167
10	BC1	SOFTWARE	ARG C:85 , LEU C:86 , GLY C:87 , ARG C:88 , THR C:120	BINDING SITE FOR RESIDUE SO4 C 166
11	BC2	SOFTWARE	LEU B:4 , PRO B:6 , HIS B:93 , ARG B:97	BINDING SITE FOR RESIDUE SO4 B 168
12	BC3	SOFTWARE	ARG C:85 , ARG C:88	BINDING SITE FOR RESIDUE SO4 C 167
13	BC4	SOFTWARE	LEU C:35 , HIS C:40 , TYR C:61 , TRP C:73 , HIS D:40 , TYR D:61	BINDING SITE FOR RESIDUE DAB D 167
14	BC5	SOFTWARE	HIS A:40 , TYR A:61 , TRP A:73 , HIS B:40 , TYR B:61	BINDING SITE FOR RESIDUE DAB D 168
15	BC6	SOFTWARE	ALA A:14 , LEU A:18 , GLU A:21 , ILE A:54 , ASP A:55 , HIS A:78 , ARG A:80	BINDING SITE FOR RESIDUE GOL A 168
16	BC7	SOFTWARE	ALA C:14 , GLN C:17 , GLU C:21 , ILE C:54 , ASP C:55 , HIS C:78 , ARG C:80	BINDING SITE FOR RESIDUE GOL C 168
17	BC8	SOFTWARE	ARG B:8 , ARG B:9 , ASN B:10 , ARG D:104 , HIS D:105	BINDING SITE FOR RESIDUE GOL B 169
18	BC9	SOFTWARE	ASN A:114 , GLN A:115 , ALA A:116 , SER A:117	BINDING SITE FOR RESIDUE GOL A 169

(no "SS Bond" information available for 3D3S)

Asymmetric Unit

No.	Residues
1	Pro A:23	-	Pro A:24
2	Gly A:157	-	Pro A:158
3	Pro B:23	-	Pro B:24
4	Gly B:157	-	Pro B:158
5	Pro C:23	-	Pro C:24
6	Gly C:157	-	Pro C:158
7	Pro D:23	-	Pro D:24
8	Gly D:157	-	Pro D:158

(no "SAP(SNP)/Variant" information available for 3D3S)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	ECTA_BORPA	24-179	4	A:2-157 B:2-157 C:2-157 D:2-157

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	ECTA_BORPA	24-179	2	A:2-157 B:2-157 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	ECTA_BORPA	24-179	2	- - C:2-157 D:2-157

(no "Exon" information available for 3D3S)

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:159
 aligned with ECTA_BORPA | Q7W980 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:159
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         
           ECTA_BORPA    23 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAMLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGPF 181
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d3sA00 A:1-159  [code=3.40.630.30, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhheeee.....eeeeeeeee......eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh...eeeeeeeehhhhhh......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GNAT  PDB: A:2-157 UniProt: 24-179                                                                                                                          -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3s A   1 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAmLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEmLLRIGPF 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 |       
                                                                                                                    90-MSE                                                       152-MSE

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with ECTA_BORPA | Q7W980 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:159
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         
           ECTA_BORPA    23 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAMLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGPF 181
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d3sB00 B:1-159  [code=3.40.630.30, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhheeee.....eeeeeeeeee..eeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh..eeeeee.......------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GNAT  PDB: B:2-157 UniProt: 24-179                                                                                                                          -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3s B   1 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAmLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAF------DEmLLRIGPF 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  |    150 |       
                                                                                                                    90-MSE                                              143    150 |       
                                                                                                                                                                                 152-MSE

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with ECTA_BORPA | Q7W980 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:160
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           ECTA_BORPA    22 LRYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAMLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGPF 181
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d3sC00 C:0-159  [code=3.40.630.30, no name defined]                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhheeee.....eeeeeeeeee..eeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeee..-----------..eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GNAT  PDB: C:2-157 UniProt: 24-179                                                                                                                          -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3s C   0 LRYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAmLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFF-----------DEmLLRIGPF 159
                                     9        19        29        39        49        59        69        79        89|       99       109       119       129        |-         -| |    159
                                                                                                                     90-MSE                                         138         150 |       
                                                                                                                                                                                  152-MSE

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with ECTA_BORPA | Q7W980 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:161
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
           ECTA_BORPA    23 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAMLGHILERQECRHVRHLETTVGPDNQASRRTFAGLAGERGAHVSEQPFFDRQAFGGADHDDEMLLRIGPFTH 183
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3d3sD00 D:1-161  [code=3.40.630.30, no name defined]                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhheeee.....eeeeeeeee......eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeee----..hhhhhhhhhhhh..eeeeee.------------..eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GNAT  PDB: D:2-157 UniProt: 24-179                                                                                                                          ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3s D   1 RYHLRPPRRNDGAAIHQLVSECPPLDLNSLYAYLLLCEHHAHTCVVAESPGGRIDGFVSAYLLPTRPDVLFVWQVAVHSRARGHRLGRAmLGHILERQECRHVRHLETTV----QASRRTFAGLAGERGAHVSEQPF------------DEmLLRIGPFTH 161
                                    10        20        30        40        50        60        70        80        90       100       110    |  120       130      |  -       150 |     160 
                                                                                                                    90-MSE             110  115                   137          150 |         
                                                                                                                                                                                 152-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 '\|'

(no "SCOP Domain" information available for 3D3S)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Aminopeptidase (284)

Homologous Superfamily: [code=3.40.630.30, no name defined] (126)

Bordetella parapertussis 12822. Organism_taxid: 257311. Strain: 12822/ nctc 13253. (1)

1a	3d3sA00	A:1-159
1b	3d3sB00	B:1-159
1c	3d3sC00	C:0-159
1d	3d3sD00	D:1-161

(no "Pfam Domain" information available for 3D3S)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ECTA_BORPA | Q7W980)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0033816	diaminobutyrate acetyltransferase activity	Catalysis of the reaction: L-2,4-diaminobutyrate + acetyl-CoA = N(4)-acetyl-L-2,4-diaminobutyrate + CoA + H(+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0019491	ectoine biosynthetic process	The chemical reactions and pathways resulting in the formation of ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid), a tetrahydropyrimidine commonly synthesized by halophilic bacteria.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:157 - Pro A:158	[ RasMol ]
		Gly B:157 - Pro B:158	[ RasMol ]
		Gly C:157 - Pro C:158	[ RasMol ]
		Gly D:157 - Pro D:158	[ RasMol ]
		Pro A:23 - Pro A:24	[ RasMol ]
		Pro B:23 - Pro B:24	[ RasMol ]
		Pro C:23 - Pro C:24	[ RasMol ]
		Pro D:23 - Pro D:24	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (4, 26)

Sites (18, 18)

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Cis Peptide Bonds (8, 8)

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