3U3G - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF LC11-RNASE H1 ISOLATED FROM COMPOST BY METAGENOMIC APPROACH: INSIGHT INTO THE STRUCTURAL BASES FOR UNUSUAL ENZYMATIC PROPERTIES OF STO-RNASE H1

Authors :   T. N. Nguyen, C. Angkawidjaja, E. Kanaya, Y. Koga, K. Takano, S. Kanaya

Date :   05 Oct 11 (Deposition) - 07 Mar 12 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: D  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: A  (1x)

Keywords :   Hydrolase, Cleave The Rna Strand Of Rna/Dna Hybrid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. N. Nguyen, C. Angkawidjaja, E. Kanaya, Y. Koga, K. Takano, S. Kanaya
Activity, Stability, And Structure Of Metagenome-Derived Lc11-Rnase H1, A Homolog Of Sulfolobus Tokodaii Rnase H1
Protein Sci. V. 21 553 2012
PubMed-ID: 22389131 | Reference-DOI: 10.1002/PRO.2043

Molecule 1 - RIBONUCLEASE H
	Chains	:	D, B, C, A
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET25B
	Expression System Strain	:	MIC2067(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	UNCULTURED ORGANISM
	Organism Taxid	:	155900
	Synonym	:	RNASE H1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:				D
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UNL	-1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UNL	-1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UNL	-1	Ligand/Ion	UNKNOWN LIGAND

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	UNL	1	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS C:137 , ALA C:138 , SER C:140 , HOH C:394 , HOH C:477	BINDING SITE FOR RESIDUE CL C 201
2	AC2	SOFTWARE	ASP A:9 , GLY A:10 , GLU A:49 , HOH A:394 , HOH A:444 , HOH A:498	BINDING SITE FOR RESIDUE CL A 201

(no "SS Bond" information available for 3U3G)

Asymmetric Unit

No.	Residues
1	Asn D:15	-	Pro D:16
2	Asn B:15	-	Pro B:16
3	Asn C:15	-	Pro C:16
4	Asn A:15	-	Pro A:16

(no "SAP(SNP)/Variant" information available for 3U3G)

(no "PROSITE Motif" information available for 3U3G)

(no "Exon" information available for 3U3G)

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:140
 aligned with E0X767_9ZZZZ | E0X767 from UniProtKB/TrEMBL  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         E0X767_9ZZZZ     1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
               SCOP domains d3u3ga_ A: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u3g A   1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with E0X767_9ZZZZ | E0X767 from UniProtKB/TrEMBL  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         E0X767_9ZZZZ     1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
               SCOP domains d3u3gb_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u3g B   1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain C from PDB  Type:PROTEIN  Length:140
 aligned with E0X767_9ZZZZ | E0X767 from UniProtKB/TrEMBL  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         E0X767_9ZZZZ     1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
               SCOP domains d3u3gc_ C: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeeee....eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u3g C   1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain D from PDB  Type:PROTEIN  Length:140
 aligned with E0X767_9ZZZZ | E0X767 from UniProtKB/TrEMBL  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
         E0X767_9ZZZZ     1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
               SCOP domains d3u3gd_ D: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeeeee.....eeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u3g D   1 MNKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAIDKALS 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

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: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: automated matches (127)

Protein domain: automated matches (127)

uncultured organism [TaxId: 155900] (1)

1a	d3u3ga_	A:
1b	d3u3gb_	B:
1c	d3u3gc_	C:
1d	d3u3gd_	D:

(no "CATH Domain" information available for 3U3G)

(no "Pfam Domain" information available for 3U3G)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (E0X767_9ZZZZ | E0X767)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:15 - Pro A:16	[ RasMol ]
		Asn B:15 - Pro B:16	[ RasMol ]
		Asn C:15 - Pro C:16	[ RasMol ]
		Asn D:15 - Pro D:16	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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		Biological Unit 4	[ Jena3D ]

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Access by PDB/NDB ID
	3u3g
		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
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Access by UniProt ID/Accession number
	E0X767_9ZZZZ \| E0X767
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	3.1.26.4
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	E0X767_9ZZZZ \| E0X767
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UniProtKB/TrEMBL
	E0X767_9ZZZZ \| E0X767	:	4h8k

(no "Related Entries Specified in the PDB File" available for 3U3G)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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