2GO1 - JenaLib

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Title :   NAD-DEPENDENT FORMATE DEHYDROGENASE FROM PSEUDOMONAS SP.101

Authors :   E. V. Filippova, K. M. Polyakov, T. V. Tikhonova, T. N. Stekhanova, K. M. V. O. Popov

Date :   12 Apr 06 (Deposition) - 02 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Oxidoreductase (Aldehude (D), Nad+(A)), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. V. Filippova, K. M. Polyakov, T. V. Tikhonova, T. N. Stekhanova, K. M. Boiko, V. O. Popov
Structure Of A New Crystal Modification Of The Bacterial Nad-Dependent Formate Dehydrogenase With A Resolution Of 2. A
Crystallography Reports V. 50 796 2005
PubMed: search | Reference-DOI: 10.1134/1.2049398

Molecule 1 - NAD-DEPENDENT FORMATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.2.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PFDH8A
	Expression System Strain	:	BL2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	33067
	Strain	:	101
	Synonym	:	FORMATE DEHYDROGENASE, FDH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:200 , ARG A:201 , ILE A:202 , HOH A:459 , HOH A:517	BINDING SITE FOR RESIDUE SO4 A 401

(no "SS Bond" information available for 2GO1)

Asymmetric Unit

No.	Residues
1	Phe A:311	-	Pro A:312
2	Gln A:313	-	Pro A:314

(no "SAP(SNP)/Variant" information available for 2GO1)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	FDH_PSESR	195-222	1	A:194-221
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	FDH_PSESR	245-267	1	A:244-266
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	FDH_PSESR	274-290	1	A:273-289

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	FDH_PSESR	195-222	2	A:194-221
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	FDH_PSESR	245-267	2	A:244-266
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	FDH_PSESR	274-290	2	A:273-289

(no "Exon" information available for 2GO1)

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:374
 aligned with FDH_PSESR | P33160 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:374
                                    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       281       291       301       311       321       331       341       351       361       371    
            FDH_PSESR     2 AKVLCVLYDDPVDGYPKTYARDDLPKIDHYPGGQTLPTPKAIDFTPGQLLGSVSGELGLRKYLESNGHTLVVTSDKDGPDSVFERELVDADVVISQPFWPAYLTPERIAKAKNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDEYLIVQGGALA 375
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2go1A01 A:1-145,A:336-374 NAD(P)-binding Rossmann-like Domain                                                                                    2go1A02 A:146-335 NAD(P)-binding Rossmann-like Domain                                                                                                                                         2go1A01 A:1-145,A:336-374               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee................................................hhhhhhhhhhhh..eeeee.......hhhhhhhh...eeee........hhhhhhhh....eeee........hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eeeee..hhhhhhhhhhhhhhh.eeeee.....hhhhhhhh..ee..hhhhhhhhh.eeee...............hhhhh...eeeee..hhhhhhhhhhhhhhhh..eeeeee...........hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.......eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ----------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2go1 A   1 AKVLCVLYDDPVDGYPKTYARDDLPKIDHYPGGQTLPTPKAIDFTPGQLLGSVSGELGLRKYLESNGHTLVVTSDKDGPDSVFERELVDADVVISQPFWPAYLTPERIAKAKNLKLALTAGIGSDHVDLQSAIDRNVTVAEVTYCNSISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDHPWRTMPYNGMTPHISGTTLTAQARYAAGTREILECFFEGRPIRDEYLIVQGGALA 374
                                    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       370

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 2GO1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

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

101 (Pseudomonas sp) (4)

1a	2go1A02	A:146-335
1b	2go1A01	A:1-145,A:336-374

(no "Pfam Domain" information available for 2GO1)

Asymmetric Unit(hide GO term definitions)

Chain A (FDH_PSESR | P33160)

molecular function
	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:0008863	formate dehydrogenase (NAD+) activity	Catalysis of the reaction: formate + NAD(+) = CO(2) + NADH.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

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	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:313 - Pro A:314	[ RasMol ]
		Phe A:311 - Pro A:312	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	2go1
		Family and Domain Information	:	ProDom \| SYSTERS
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		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
	FDH_PSESR \| P33160
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	1.2.1.2
		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
		Ligand-protein Contacts	:	LPC
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	FDH_PSESR \| P33160
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UniProtKB/Swiss-Prot
	FDH_PSESR \| P33160	:	2gug 2nac 2nad

2nac	THE APO FORM OF THE SAME PROTEIN
2nad	THE HOLO FORM OF THE SAME PROTEIN COMPLEXED WITH NAD AND AZIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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