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Description

Title :   CRYSTAL STRUCTURE OF A VINYL-4-REDUCTASE FAMILY PROTEIN (MJ_1460) FROM METHANOCALDOCOCCUS JANNASCHII DSM AT 2.40 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   05 Feb 07 (Deposition) - 20 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein Mj_1460 (1592102) From Methanococcus Jannaschii At 2. 30 A Resolution
To Be Published
PubMed: search

Compounds

Molecule 1 - HYPOTHETICAL PROTEIN MJ1460
	Atcc	:	43067
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	V4R DOMAIN
	Gene	:	1592102, MJ1460
	Mutation	:	YES
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII DSM 2661
	Organism Taxid	:	243232
	Strain	:	DSM 2661, JAL-1, JCM 10045, NBRC 100440

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (5, 10)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	ZN	-1	Ligand/Ion	ZINC ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:19 , GLU A:128 , GLU A:129 , HOH A:183 , HOH A:184 , HOH A:186	BINDING SITE FOR RESIDUE CA A 163
2	AC2	SOFTWARE	GLU A:19 , GLU A:23 , GLU A:129 , HOH A:181 , HOH A:193 , HOH A:198	BINDING SITE FOR RESIDUE CA A 164
3	AC3	SOFTWARE	SER A:24 , LYS A:25 , MSE A:29 , TYR A:106 , HOH A:190	BINDING SITE FOR RESIDUE CL A 165
4	AC4	SOFTWARE	HIS A:116 , GLU A:139 , CYS A:142 , CYS A:150	BINDING SITE FOR RESIDUE ZN A 166
5	AC5	SOFTWARE	PHE A:32 , TYR A:106	BINDING SITE FOR RESIDUE EDO A 167
6	AC6	SOFTWARE	SER A:64 , PRO A:65 , GLU A:129	BINDING SITE FOR RESIDUE EDO A 168
7	AC7	SOFTWARE	ASN A:138 , GLU A:139	BINDING SITE FOR RESIDUE EDO A 169

SS Bonds (0, 0)

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

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Pro A:95	-	Pro A:96

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	Y1460_METJA	91-97	1	A:91-97

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	Y1460_METJA	91-97	2	A:91-97

Exons (0, 0)

(no "Exon" information available for 2OSD)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:150
 aligned with Y1460_METJA | Q58855 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:152
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154  
          Y1460_METJA     5 EKIFPDILEAIRNEEIIKESKKIPMPYFGLFALVIFDKVKELGSETSLYEIGEEFGKMLSPKNIEELKKIFKLMNFGDLEIDENKILLKNPPYKIKLSNPPYQWVSKEEPIHDFIAGILAGCLEEIFKKKFVVNEVECVSQGKDKCVFEVKE 156
               SCOP domains d2osda1 A:5-156 Hypothetical protein MJ1  460                                                                                                            SCOP domains
               CATH domains 2osdA00 A:5-156 Trafficking protein part  icle complex subunit 3                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------V4R-2osdA01 A:96-156                                          Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh--....hhhhhhhhhhhhhh..hhhhhhhhhhhhh..eee.hhhhhhh....eeeeee.............hhhhhhhhhhhhhhhhh...eeeeeehhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------N6_MTAS----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osd A   5 EKIFPDILEAIRNEEIIKESKKIPmPYFGLFALVIFDKVK--GSETSLYEIGEEFGKmLSPKNIEELKKIFKLmNFGDLEIDENKILLKNPPYKIKLSNPPYQWVSKEEPIHDFIAGILAGCLEEIFYYYFVVNEVECVSQGKDKCVFEVKE 156
                                    14        24    |   34        44  |     54       |64        74   |    84        94       104       114       124       134       144       154  
                                                   29-MSE         44 47             62-MSE          78-MSE

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ligand-binding domain in the NO signalling and Golgi transport (29)

Superfamily: Ligand-binding domain in the NO signalling and Golgi transport (29)

Family: MJ1460-like (2)

Protein domain: Hypothetical protein MJ1460 (2)

Methanococcus jannaschii [TaxId: 2190] (2)

d2osda1

A:5-156

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Muramoyl-pentapeptide Carboxypeptidase; domain 2 (24)

Homologous Superfamily: Trafficking protein particle complex subunit 3 (11)

Methanocaldococcus jannaschii dsm 2661. Organism_taxid: 243232. Strain: dsm 2661, jal-1, jcm 10045, nbrc 100440. (2)

2osdA00

A:5-156

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HNOX-like (7)

Family: V4R (2)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (2)

V4R-2osdA01

A:96-156

Gene Ontology (0, 0)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2OSD)

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		Pro A:95 - Pro A:96	[ RasMol ]

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Related Entries

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UniProtKB/Swiss-Prot
	Y1460_METJA \| Q58855	:	2oso

Related Entries Specified in the PDB File

2oso	CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII DSM 2661 COMPLETE GENOME (1592102) FROM METHANOCOCCUS JANNASCHII AT 1.90 A RESOLUTION