1P74 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) FROM HAEMOPHILUS INFLUENZAE

Authors :   S. Ye, F. Von Delft, A. Brooun, M. W. Knuth, R. V. Swanson, D. E. Mcree

Date :   30 Apr 03 (Deposition) - 12 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Shikimate Dehydrogenase, Haemophilus Influenzae, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ye, F. Von Delft, A. Brooun, M. W. Knuth, R. V. Swanson, D. E. Mcree
The Crystal Structure Of Shikimate Dehydrogenase (Aroe) Reveals A Unique Nadph Binding Mode
J. Bacteriol. V. 185 4144 2003
PubMed-ID: 12837789 | Reference-DOI: 10.1128/JB.185.14.4144-4151.2003
(for further references see the PDB file header)

Molecule 1 - SHIKIMATE 5-DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSX12
	Expression System Strain	:	DL41
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AROE OR HI0655
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1P74)

(no "Site" information available for 1P74)

(no "SS Bond" information available for 1P74)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:9	-	Pro A:10
2	Ser A:62	-	Pro A:63
3	Asn B:9	-	Pro B:10
4	Ser B:62	-	Pro B:63

(no "SAP(SNP)/Variant" information available for 1P74)

(no "PROSITE Motif" information available for 1P74)

(no "Exon" information available for 1P74)

Asymmetric/Biological 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:267
 aligned with AROE_HAEIN | P43876 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:272
                                    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  
           AROE_HAEIN     1 MDLYAVWGNPIAQSKSPLIQNKLAAQTHQTMEYIAKLGDLDAFEQQLLAFFEEGAKGCNITSPFKERAYQLADEYSQRAKLAEACNTLKKLDDGKLYADNTDGIGLVTDLQRLNWLRPNQHVLILGAGGATKGVLLPLLQAQQNIVLANRTFSKTKELAERFQPYGNIQAVSMDSIPLQTYDLVINATSAGLSGGTASVDAEILKLGSAFYDMQYAKGTDTPFIALCKSLGLTNVSDGFGMLVAQAAHSFHLWRGVMPDFVSVYEQLKKAML 272
               SCOP domains d1p74a2 A:1-101 Shikimate 5-dehydrogenase AroE                                                       d1p74a1 A:102-272 Shikimate 5-dehydrogenase AroE                                                                                                                            SCOP domains
               CATH domains 1p74A01 A:1-114,A:238-272 Leucine Dehydrogenase, chain A, domain 1                                                1p74A02 A:115-237 NAD(P)-binding Rossmann-like Domain                                                                      1p74A01 A:1-114,A:238-272           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeee...hhhhhhh...eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh.eeeee..........eeee.....-----...hhhhhh....eee........hhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p74 A   1 MDLYAVWGNPIAQSKSPLIQNKLAAQTHQTMEYIAKLGDLDAFEQQLLAFFEEGAKGCNITSPFKERAYQLADEYSQRAKLAEACNTLKKLDDGKLYADNTDGIGLVTDLQRLNWLRPNQHVLILGAGGATKGVLLPLLQAQQNIVLANRTFSKTKELAERFQPYGNIQAVSMDSIPLQTYDLVINATSAG-----ASVDAEILKLGSAFYDMQYAKGTDTPFIALCKSLGLTNVSDGFGMLVAQAAHSFHLWRGVMPDFVSVYEQLKKAML 272
                                    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  
                                                                                                                                                                                                                        191   197

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with AROE_HAEIN | P43876 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:272
                                    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  
           AROE_HAEIN     1 MDLYAVWGNPIAQSKSPLIQNKLAAQTHQTMEYIAKLGDLDAFEQQLLAFFEEGAKGCNITSPFKERAYQLADEYSQRAKLAEACNTLKKLDDGKLYADNTDGIGLVTDLQRLNWLRPNQHVLILGAGGATKGVLLPLLQAQQNIVLANRTFSKTKELAERFQPYGNIQAVSMDSIPLQTYDLVINATSAGLSGGTASVDAEILKLGSAFYDMQYAKGTDTPFIALCKSLGLTNVSDGFGMLVAQAAHSFHLWRGVMPDFVSVYEQLKKAML 272
               SCOP domains d1p74b2 B:1-101 Shikimate 5-dehydrogenase AroE                                                       d1p74b1 B:102-272 Shikimate 5-dehydrogenase AroE                                                                                                                            SCOP domains
               CATH domains 1p74B01 B:1-114,B:238-272 Leucine Dehydrogenase, chain A, domain 1                                                1p74B02 B:115-237 NAD(P)-binding Rossmann-like Domain                                                                      1p74B01 B:1-114,B:238-272           CATH domains
           Pfam domains (1) -----Shikimate_dh_N-1p74B03 B:6-88                                                      ---------------------Shikimate_DH-1p74B01 B:110-217                                                                              ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Shikimate_dh_N-1p74B04 B:6-88                                                      ---------------------Shikimate_DH-1p74B02 B:110-217                                                                              ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeee...hhhhhhh...eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh.eeeee.hhh......eeee....------...hhhhhh....eee........hhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p74 B   1 MDLYAVWGNPIAQSKSPLIQNKLAAQTHQTMEYIAKLGDLDAFEQQLLAFFEEGAKGCNITSPFKERAYQLADEYSQRAKLAEACNTLKKLDDGKLYADNTDGIGLVTDLQRLNWLRPNQHVLILGAGGATKGVLLPLLQAQQNIVLANRTFSKTKELAERFQPYGNIQAVSMDSIPLQTYDLVINATSA------ASVDAEILKLGSAFYDMQYAKGTDTPFIALCKSLGLTNVSDGFGMLVAQAAHSFHLWRGVMPDFVSVYEQLKKAML 272
                                    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  
                                                                                                                                                                                                                       190    197

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Leucine Dehydrogenase; Chain A, domain 1 (52)

Homologous Superfamily: Leucine Dehydrogenase, chain A, domain 1 (52)

Haemophilus influenzae. Organism_taxid: 727. (3)

1a	1p74A01	A:1-114,A:238-272
1b	1p74B01	B:1-114,B:238-272

Topology: Rossmann fold (7312)

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

Haemophilus influenzae. Organism_taxid: 727. (14)

2a	1p74A02	A:115-237
2b	1p74B02	B:115-237

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AROE_HAEIN | P43876)

molecular function
	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: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:0004764	shikimate 3-dehydrogenase (NADP+) activity	Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
biological process
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	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:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	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:0019632	shikimate metabolic process	The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1p74)

	Sites
(no "Sites" information available for 1p74)

	Cis Peptide Bonds
		Asn A:9 - Pro A:10	[ RasMol ]
		Asn B:9 - Pro B:10	[ RasMol ]
		Ser A:62 - Pro A:63	[ RasMol ]
		Ser B:62 - Pro B:63	[ RasMol ]

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Access by PDB/NDB ID
	1p74
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	AROE_HAEIN \| P43876
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
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	1.1.1.25
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	AROE_HAEIN \| P43876
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UniProtKB/Swiss-Prot
	AROE_HAEIN \| P43876	:	1p77

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (8, 8)

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