1BRM - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI

Authors :   A. T. Hadfield, G. Kryger, J. Ouyang, D. Ringe, G. A. Petsko, R. E. Viola

Date :   24 Aug 98 (Deposition) - 22 Jun 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Crystal Structure, Dehydrogenase, Escherichia Coli, Enzyme, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Hadfield, G. Kryger, J. Ouyang, G. A. Petsko, D. Ringe, R. Viola
Structure Of Aspartate-Beta-Semialdehyde Dehydrogenase From Escherichia Coli, A Key Enzyme In The Aspartate Family Of Amino Acid Biosynthesis.
J. Mol. Biol. V. 289 991 1999
PubMed-ID: 10369777 | Reference-DOI: 10.1006/JMBI.1999.2828
(for further references see the PDB file header)

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
	Chains	:	A, B, C
	EC Number	:	1.2.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	JM109
	Expression System Gene	:	ASD
	Expression System Plasmid	:	PGEM
	Expression System Taxid	:	562
	Gene	:	ASD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ASADH, ASDH

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1BRM)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AT1	UNKNOWN	CYS A:135 , HIS A:274 , ARG A:267 , GLN A:162	ACTIVE SITE IDENTIFIED FROM MODIFIED CYS.
2	AT2	UNKNOWN	CYS B:135 , HIS B:274 , ARG B:267 , GLN B:162	ACTIVE SITE IDENTIFIED FROM MODIFIED CYS.
3	AT3	UNKNOWN	CYS C:135 , HIS C:274 , ARG C:267 , GLN C:162	ACTIVE SITE IDENTIFIED FROM MODIFIED CYS.

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS_ECOLI	261-275	3	A:261-275 B:261-275 C:261-275

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS_ECOLI	261-275	2	A:261-275 B:261-275 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS_ECOLI	261-275	2	- - C:261-275

(no "Exon" information available for 1BRM)

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:356
 aligned with DHAS_ECOLI | P0A9Q9 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:367
                                    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       360       
           DHAS_ECOLI     1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA 367
               SCOP domains d1brma1 A:1-133,A:355-367 Aspartate beta-semialdehyde dehydrogenase                                                                  d1brma2 A:134-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                  d1brma1       SCOP domains
               CATH domains 1brmA01 A:1-134,A:351-367 NAD(P)-binding Rossmann-like Domain                                                                         1brmA02 A:135-350 Dihydrodipicolinate Reductase; domain 2                                                                                                                                                               1brmA01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh......eeeee..hhh....................hhhhh...eeee...hhhhhhhhhhhh......eeee..........eeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....................-----------...hhhhhhh.......eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhh..........hhhhhhh..hhhh...................eeeeeeeee.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brm A   1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWID-----------WKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA 367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230|        -  |    250       260       270       280       290       300       310       320       330       340       350       360       
                                                                                                                                                                                                                                                                231         243

Chain B from PDB  Type:PROTEIN  Length:357
 aligned with DHAS_ECOLI | P0A9Q9 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:367
                                    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       360       
           DHAS_ECOLI     1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA 367
               SCOP domains d1brmb1 B:1-133,B:355-367 Aspartate beta-semialdehyde dehydrogenase                                                                  d1brmb2 B:134-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                  d1brmb1       SCOP domains
               CATH domains 1brmB01 B:1-134,B:351-367 NAD(P)-binding Rossmann-like Domain                                                                         1brmB02 B:135-350 Dihydrodipicolinate Reductase; domain 2                                                                                                                                                               1brmB01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhh..hhhheeeee.........................hhhhh...eeee...hhhhhhhhhhhhhh....eeee..........eeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhh..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.....................----------....hhhhhhh.......eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhh..........hhhhhhh..hhhh...................eeeeeeeee.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brm B   1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWID----------EWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA 367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230|        - |     250       260       270       280       290       300       310       320       330       340       350       360       
                                                                                                                                                                                                                                                                231        242

Chain C from PDB  Type:PROTEIN  Length:359
 aligned with DHAS_ECOLI | P0A9Q9 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:367
                                    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       360       
           DHAS_ECOLI     1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA 367
               SCOP domains d1brmc1 C:1-133,C:355-367 Aspartate beta-semialdehyde dehydrogenase                                                                  d1brmc2 C:134-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                  d1brmc1       SCOP domains
               CATH domains 1brmC01 C:1-134,C:351-367 NAD(P)-binding Rossmann-like Domain                                                                         1brmC02 C:135-350 Dihydrodipicolinate Reductase; domain 2                                                                                                                                                               1brmC01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhh.hhh.eeeee.........................hhhhh...eeee...hhhhhhhhhhhhhh....eeee..hhh.....eeee.hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhh..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......................--------.....hhhhhhh.......eeeeeeee.....eeeeeeeeee.....hhhhhhhhhhh..........hhhhhhh..hhhh...................eeeeeeeee.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            -------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1brm C   1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDK--------EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQLA 367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |       -|      250       260       270       280       290       300       310       320       330       340       350       360       
                                                                                                                                                                                                                                                                 232      241

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dihydrodipicolinate Reductase; domain 2 (182)

Homologous Superfamily: Dihydrodipicolinate Reductase; domain 2 (178)

Escherichia coli. Organism_taxid: 562. (8)

1a	1brmA02	A:135-350
1b	1brmB02	B:135-350
1c	1brmC02	C:135-350

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Escherichia coli. Organism_taxid: 562. (48)

2a	1brmA01	A:1-134,A:351-367
2b	1brmB01	B:1-134,B:351-367
2c	1brmC01	C:1-134,C:351-367

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DHAS_ECOLI | P0A9Q9)

molecular function
	GO:0003942	N-acetyl-gamma-glutamyl-phosphate reductase activity	Catalysis of the reaction: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetyl-5-glutamyl phosphate + NADPH + H+.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0004073	aspartate-semialdehyde dehydrogenase activity	Catalysis of the reaction: L-aspartate 4-semialdehyde + NADP(+) + phosphate = 4-phospho-L-aspartate + H(+) + NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
	GO:0071266	'de novo' L-methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid, from simpler components.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009090	homoserine biosynthetic process	The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
	GO:0009097	isoleucine biosynthetic process	The chemical reactions and pathways resulting in the formation of isoleucine, (2R,3R)-2-amino-3-methylpentanoic acid.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0009088	threonine biosynthetic process	The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (3, 3)

SS Bonds (0, 0)

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