2ZZA - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   MORITELLA PROFUNDA DIHYDROFOLATE REDUCTASE COMPLEX WITH NADP+ AND FOLATE

Authors :   K. Hata, T. Tanaka, C. Murakami, E. Ohmae, K. Gekko, Y. Shiro, K. Akasaka

Date :   06 Feb 09 (Deposition) - 23 Feb 10 (Release) - 23 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dihydrofolate Reductase, Folic Acid, Nadp, Deep-Sea, High Pressure, Low Temperature, Moritella Profunda, Piezophilic, Psychrophilic, Psychropiezophilic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Hata, T. Tanaka, C. Murakami, E. Ohmae, K. Gekko, Y. Shiro, K. Akasaka
Moritella Profunda Dihydrofolate Reductase Complex With Nadp+ And Folate
To Be Published
PubMed: search

Molecule 1 - DIHYDROFOLATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.5.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC118
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DYRA
	Organism Scientific	:	MORITELLA PROFUNDA
	Organism Taxid	:	111291
	Strain	:	2674T

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FOL	2	Ligand/Ion	FOLIC ACID
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FOL	1	Ligand/Ion	FOLIC ACID
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	FOL	1	Ligand/Ion	FOLIC ACID
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:7 , ALA A:8 , ILE A:15 , GLY A:16 , ASN A:19 , LYS A:20 , MET A:21 , GLY A:44 , ARG A:45 , ASN A:46 , THR A:47 , LEU A:63 , SER A:64 , ARG A:65 , ALA A:78 , ILE A:96 , GLY A:98 , ALA A:99 , THR A:100 , ILE A:101 , TYR A:102 , GLN A:104 , THR A:125 , FOL A:164 , HOH A:196 , HOH A:234 , HOH A:299 , HOH A:302 , HOH A:304 , HOH A:309 , ARG B:65 , NAP B:163 , HOH B:251	BINDING SITE FOR RESIDUE NAP A 163
2	AC2	SOFTWARE	ILE A:6 , ALA A:7 , ALA A:8 , MET A:21 , GLU A:28 , LEU A:29 , PHE A:32 , LYS A:33 , ARG A:58 , ILE A:96 , NAP A:163 , HOH A:172 , HOH A:237 , HOH A:293 , HOH A:302 , HOH A:318	BINDING SITE FOR RESIDUE FOL A 164
3	AC3	SOFTWARE	ARG A:34 , PHE A:155 , ARG B:34 , TYR B:143 , PHE B:155	BINDING SITE FOR RESIDUE 1PE A 165
4	AC4	SOFTWARE	ARG A:65 , NAP A:163 , HOH A:290 , ALA B:7 , ALA B:8 , ILE B:15 , GLY B:16 , LEU B:17 , ASN B:19 , LYS B:20 , MET B:21 , GLY B:44 , ARG B:45 , ASN B:46 , THR B:47 , SER B:50 , LEU B:63 , SER B:64 , ARG B:65 , ALA B:78 , ILE B:96 , GLY B:98 , ALA B:99 , THR B:100 , ILE B:101 , TYR B:102 , GLN B:104 , THR B:125 , FOL B:164 , HOH B:166 , HOH B:172 , HOH B:186 , HOH B:194 , HOH B:211 , HOH B:243	BINDING SITE FOR RESIDUE NAP B 163
5	AC5	SOFTWARE	ILE B:6 , ALA B:7 , ALA B:8 , MET B:21 , GLU B:28 , LEU B:29 , PHE B:32 , LYS B:33 , LEU B:55 , ARG B:58 , ILE B:96 , NAP B:163 , HOH B:167 , HOH B:181 , HOH B:193 , HOH B:243 , HOH B:267 , HOH B:279	BINDING SITE FOR RESIDUE FOL B 164

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

Asymmetric Unit

No.	Residues
1	Gly B:97	-	Gly B:98

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

(no "PROSITE Motif" information available for 2ZZA)

(no "Exon" information available for 2ZZA)

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:161
 aligned with Q70YQ6_MORPR | Q70YQ6 from UniProtKB/TrEMBL  Length:162

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q70YQ6_MORPR     1 MIVSMIAALANNRVIGLDNKMPWHLPAELQLFKRATLGKPIVMGRNTFESIGRPLPGRLNIVLSRQTDYQPEGVTVVATLEDAVVAAGDVEELMIIGGATIYNQCLAAADRLYLTHIELTTEGDTWFPDYEQYNWQEIEHESYAADDKNPHNYRFSLLERV 161
               SCOP domains d2zzaa_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 2zzaA00 A:1-161 Dihydrofolate Reductase, subunit A                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeehhh.eee........hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee...........eee.hhhhhhhhhh...eeee..hhhhhhhhhhhh.eeeeeee.......ee..hhhhheeeeeeeeee.........eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zza A   1 VIVSMIAALANNRVIGLDNKMPWHLPAELQLFKRATLGKPIVMGRNTFESIGRPLPGRLNIVLSRQTDYQPEGVTVVATLEDAVVAAGDVEELMIIGGATIYNQCLAAADRLYLTHIELTTEGDTWFPDYEQYNWQEIEHESYAADDKNPHNYRFSLLERV 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q70YQ6_MORPR | Q70YQ6 from UniProtKB/TrEMBL  Length:162

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q70YQ6_MORPR     1 MIVSMIAALANNRVIGLDNKMPWHLPAELQLFKRATLGKPIVMGRNTFESIGRPLPGRLNIVLSRQTDYQPEGVTVVATLEDAVVAAGDVEELMIIGGATIYNQCLAAADRLYLTHIELTTEGDTWFPDYEQYNWQEIEHESYAADDKNPHNYRFSLLERV 161
               SCOP domains d2zzab_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains 2zzaB00 B:1-161 Dihydrofolate Reductase, subunit A                                                                                                                CATH domains
           Pfam domains (1) -DHFR_1-2zzaB01 B:2-160                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) -DHFR_1-2zzaB02 B:2-160                                                                                                                                         - Pfam domains (2)
         Sec.struct. author .eeeeeeeehhh.eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee...........eee.hhhhhhhhh....eeee..hhhhhhhhhhhh.eeeeeee.......ee..hhhhheeeeeeeeee.........eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zza B   1 VIVSMIAALANNRVIGLDNKMPWHLPAELQLFKRATLGKPIVMGRNTFESIGRPLPGRLNIVLSRQTDYQPEGVTVVATLEDAVVAAGDVEELMIIGGATIYNQCLAAADRLYLTHIELTTEGDTWFPDYEQYNWQEIEHESYAADDKNPHNYRFSLLERV 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Dihydrofolate reductase-like (332)

Superfamily: Dihydrofolate reductase-like (332)

Family: automated matches (76)

Protein domain: automated matches (76)

Moritella profunda [TaxId: 111291] (3)

1a	d2zzaa_	A:
1b	d2zzab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Dihydrofolate Reductase, subunit A (200)

Homologous Superfamily: Dihydrofolate Reductase, subunit A (200)

Moritella profunda. Organism_taxid: 111291. Strain: 2674t. (1)

1a	2zzaA00	A:1-161
1b	2zzaB00	B:1-161

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DHFred (95)

Family: DHFR_1 (89)

Moritella profunda (1)

1a	DHFR_1-2zzaB01	B:2-160
1b	DHFR_1-2zzaB02	B:2-160

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q70YQ6_MORPR | Q70YQ6)

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:0004146	dihydrofolate reductase activity	Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
biological process
	GO:0006545	glycine biosynthetic process	The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	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:0046654	tetrahydrofolate biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		1PE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly B:97 - Gly B:98	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2zza
		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
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q70YQ6_MORPR \| Q70YQ6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	1.5.1.3
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q70YQ6_MORPR \| Q70YQ6
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q70YQ6_MORPR \| Q70YQ6	:	3ia4 3ia5

(no "Related Entries Specified in the PDB File" available for 2ZZA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File