1YS4 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF ASPARTATE-SEMIALDEHYDE DEHYDROGENASE FROM METHANOCOCCUS JANNASCHII

Authors :   C. R. Faehnle, J. F. Ohren, R. E. Viola

Date :   07 Feb 05 (Deposition) - 01 Nov 05 (Release) - 29 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

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

Keywords :   Oxidoreductase, Asadh (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. R. Faehnle, J. F. Ohren, R. E. Viola
A New Branch In The Family: Structure Of Aspartate-Beta-Semialdehyde Dehydrogenase From Methanococcu Jannaschii
J. Mol. Biol. V. 353 1055 2005
PubMed-ID: 16225889 | Reference-DOI: 10.1016/J.JMB.2005.09.027

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.2.1.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET41A
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ASD
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	ASA DEHYDROGENASE, ASADH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 26)

No.	Name	Count	Type	Full Name
1	MLA	4	Ligand/Ion	MALONIC ACID
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (3, 26)

No.	Name	Count	Type	Full Name
1	MLA	4	Ligand/Ion	MALONIC ACID
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (3, 52)

No.	Name	Count	Type	Full Name
1	MLA	8	Ligand/Ion	MALONIC ACID
2	MSE	40	Mod. Amino Acid	SELENOMETHIONINE
3	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , THR A:17 , GLY A:18 , SER A:19 , VAL A:20 , ALA A:41 , SER A:42 , SER A:45 , THR A:74 , PRO A:92 , LEU A:95 , ASN A:113 , SER A:187 , GLY A:188 , ALA A:189 , GLY A:190 , ASN A:333 , THR A:334 , ALA A:338 , MLA A:904 , HOH A:934 , HOH A:983 , HOH A:986 , HOH A:995 , HOH A:1025 , HOH A:1038 , HOH A:1068	BINDING SITE FOR RESIDUE NAP A 900
2	AC2	SOFTWARE	GLY B:15 , THR B:17 , GLY B:18 , SER B:19 , VAL B:20 , ALA B:41 , SER B:42 , SER B:45 , THR B:74 , ALA B:90 , LEU B:91 , PRO B:92 , LEU B:95 , ASN B:113 , GLY B:188 , GLY B:190 , ASN B:333 , THR B:334 , ALA B:338 , MLA B:902 , HOH B:944 , HOH B:986 , HOH B:990 , HOH B:1011 , HOH B:1020 , HOH B:1051 , HOH B:1055 , HOH B:1092 , HOH B:1094 , HOH B:1121	BINDING SITE FOR RESIDUE NAP B 901
3	AC3	SOFTWARE	ASN B:113 , ARG B:118 , ASN B:156 , CYS B:157 , LYS B:213 , NAP B:901 , HOH B:951 , HOH B:1020	BINDING SITE FOR RESIDUE MLA B 902
4	AC4	SOFTWARE	PHE A:206 , ILE A:207 , ASN A:209 , GLU A:210 , GLU A:211 , GLU A:212 , HOH A:914 , HOH A:964 , HOH A:1096 , ARG B:316	BINDING SITE FOR RESIDUE MLA A 903
5	AC5	SOFTWARE	SER A:115 , ARG A:118 , ASN A:156 , CYS A:157 , LYS A:213 , NAP A:900 , HOH A:922 , HOH A:940 , HOH A:1025	BINDING SITE FOR RESIDUE MLA A 904
6	AC6	SOFTWARE	ARG A:316 , PHE B:206 , ILE B:207 , ASN B:209 , GLU B:210 , GLU B:211 , GLU B:212 , HOH B:918 , HOH B:989 , HOH B:1053 , HOH B:1060 , HOH B:1066	BINDING SITE FOR RESIDUE MLA B 905

(no "SS Bond" information available for 1YS4)

Asymmetric Unit

No.	Residues
1	Arg A:297	-	Pro A:298
2	Arg B:297	-	Pro B:298

(no "SAP(SNP)/Variant" information available for 1YS4)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS_METJA	237-251	2	A:237-251 B:237-251

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS_METJA	237-251	2	A:237-251 B:237-251

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASD	PS01103	Aspartate-semialdehyde dehydrogenase signature.	DHAS_METJA	237-251	4	A:237-251 B:237-251

(no "Exon" information available for 1YS4)

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:348
 aligned with DHAS_METJA | Q57658 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:348
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346        
           DHAS_METJA     7 MKIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENIKDMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVIPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSGAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNEGNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI 354
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh....eeeeeeee.......hhhhhh.................ee....hhhhh...eeee..hhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhh....hhhhhh........hhhhhhhhhhhhhh.eee..eee....eeeee.........eeeeeeee.....hhhhhhhhhhhh..............eee.......hhhhhhhhhhhh.eeeeeeee.....eeeeeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ys4 A   7 mKIKVGVLGATGSVGQRFVQLLADHPmFELTALAASERSAGKKYKDACYWFQDRDIPENIKDmVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRmEEDVPLVIPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPImDKFGLEAVFIATmQAVSGAGYNGVPSmAILDNLIPFIKNEEEKmQTESLKLLGTLKDGKVELANFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVmDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNEGNGmSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI 354
                            |       16        26      | 36        46        56        66  |     76        86        96       106       116  |    126       136       146       156       166   |   176      |186       196|      206       216       226       236       246       256       266    |  276       286       296       306   |   316       326       336       346        
                            |                        33-MSE                              69-MSE                                           119-MSE                                            170-MSE      183-MSE       197-MSE          214-MSE                                                  271-MSE                                310-MSE                                        
                            7-MSE

Chain B from PDB  Type:PROTEIN  Length:348
 aligned with DHAS_METJA | Q57658 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:348
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346        
           DHAS_METJA     7 MKIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENIKDMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVIPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSGAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNEGNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI 354
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---Semialdhyde_dh-1ys4B03 B:10-138                                                                                                  ---------------------------Semialdhyde_dhC-1ys4B01 B:166-336                                                                                                                                          ------------------ Pfam domains (1)
           Pfam domains (2) ---Semialdhyde_dh-1ys4B04 B:10-138                                                                                                  ---------------------------Semialdhyde_dhC-1ys4B02 B:166-336                                                                                                                                          ------------------ Pfam domains (2)
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh....eeeeeeee.......hhhhhh........hhhhhh...ee............eeee..hhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhh....hhhhhh........hhhhhhhhhhhhhh.eee..eee....eeeee.........eeeeeeee.....hhhhhhhhhhhh..............eeee......hhhhhhhhhhhh.eeeeeeee.....eeeeeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ys4 B   7 mKIKVGVLGATGSVGQRFVQLLADHPmFELTALAASERSAGKKYKDACYWFQDRDIPENIKDmVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRmEEDVPLVIPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPImDKFGLEAVFIATmQAVSGAGYNGVPSmAILDNLIPFIKNEEEKmQTESLKLLGTLKDGKVELANFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVmDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNEGNGmSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI 354
                            |       16        26      | 36        46        56        66  |     76        86        96       106       116  |    126       136       146       156       166   |   176      |186       196|      206       216       226       236       246       256       266    |  276       286       296       306   |   316       326       336       346        
                            7-MSE                    33-MSE                              69-MSE                                           119-MSE                                            170-MSE      183-MSE       197-MSE          214-MSE                                                  271-MSE                                310-MSE

Legend:		→ Mismatch	(orange background)
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	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 1YS4)

(no "CATH Domain" information available for 1YS4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHAS_METJA | Q57658)

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:0006531	aspartate metabolic process	The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
	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: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: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.

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	Cis Peptide Bonds
		Arg A:297 - Pro A:298	[ RasMol ]
		Arg B:297 - Pro B:298	[ RasMol ]

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	1ys4
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1brm	ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM ESCHERICHIA COLI
1nwc	CRYSTAL STRUCTURE OF ASPARTATE-SEMIALDEHYDE DEHYDROGENASE FROM HAEMOPHILUS INFLUENZAE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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