1DIH - JenaLib

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Title :   THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE

Authors :   G. Scapin, J. S. Blanchard, J. C. Sacchettini

Date :   14 Sep 94 (Deposition) - 15 Sep 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

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

Reference :   G. Scapin, J. S. Blanchard, J. C. Sacchettini
Three-Dimensional Structure Of Escherichia Coli Dihydrodipicolinate Reductase.
Biochemistry V. 34 3502 1995
PubMed-ID: 7893645 | Reference-DOI: 10.1021/BI00011A003
(for further references see the PDB file header)

Molecule 1 - DIHYDRODIPICOLINATE REDUCTASE
	Chains	:	A
	EC Number	:	1.3.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NDP	1	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , GLY A:15 , ARG A:16 , MET A:17 , GLU A:38 , ARG A:39 , PHE A:79 , THR A:80 , ARG A:81 , GLU A:83 , GLY A:84 , GLY A:102 , THR A:103 , THR A:104 , ALA A:126 , ALA A:127 , ASN A:128 , PHE A:129 , ARG A:240 , PHE A:243	BINDING SITE FOR RESIDUE NDP A 301
2	SI1	UNKNOWN	THR A:80 , GLY A:102 , THR A:104 , ALA A:126 , ALA A:127 , PHE A:129 , ARG A:16 , MET A:17 , ARG A:81 , ARG A:240 , GLY A:12 , GLY A:15 , GLU A:38 , ARG A:39 , GLY A:84	NULL

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

Asymmetric Unit

No.	Residues
1	Ala A:166	-	Pro A:167

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAPB	PS01298	Dihydrodipicolinate reductase signature.	DAPB_ECOLI	154-171	1	A:154-171

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAPB	PS01298	Dihydrodipicolinate reductase signature.	DAPB_ECOLI	154-171	4	A:154-171

(no "Exon" information available for 1DIH)

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:272
 aligned with DAPB_ECOLI | P04036 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
           DAPB_ECOLI     2 HDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL 273
               SCOP domains d1diha1 A:2-130,A:241-273 Dihydrodipicolinate reductase                                                                          d1diha2 A:131-240 Dihydrodipicolinate reductase                                                               d1diha1 A:2-130,A:241-273         SCOP domains
               CATH domains 1dihA01 A:2-130,A:239-273 NAD(P)-binding Rossmann-like Domain                                                                    1dihA02 A:131-238 Dihydrodipicolinate Reductase; domain 2                                                   1dihA01 A:2-130,A:239-273           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhhh....eeeeee......................eeeee..........eeeee...hhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeeeeeeeee........hhhhhhhhhhhhh.......................eeeeeeeee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------DAPB              ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dih A   2 HDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL 273
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

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. (3)

1dihA02

A:131-238

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

Topology: Rossmann fold (7312)

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

Escherichia coli. Organism_taxid: 562. (49)

1dihA01

A:2-130,A:239-273

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

Asymmetric Unit(hide GO term definitions)

Chain A (DAPB_ECOLI | P04036)

molecular function
	GO:0008839	4-hydroxy-tetrahydrodipicolinate reductase	Catalysis of the reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + 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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0016726	oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	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: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: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: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.
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.

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		Ala A:166 - Pro A:167	[ RasMol ]

Biological Unit
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	1dih
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	DAPB_ECOLI \| P04036	:	1arz 1dru 1drv 1drw

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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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