3NR1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   A METAZOAN ORTHOLOG OF SPOT HYDROLYZES PPGPP AND PLAYS A ROLE IN STARVATION RESPONSES

Authors :   D. W. Sun, H. Y. Kim, K. J. Kim, Y. H. Jeon, J. Chung

Date :   30 Jun 10 (Deposition) - 08 Sep 10 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Stringent Response, Pyrophosphohydrolase, Hd (Histidine And Aspartic Acid) Family, Ppgpp Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. W. Sun, G. Lee, J. H. Lee, H. Y. Kim, H. W. Rhee, S. Y. Park, K. J. Kim, Y. Kim, B. Y. Kim, J. I. Hong, C. Park, H. E. Choy, J. H. Kim, Y. H. Jeon, J. Chung
A Metazoan Ortholog Of Spot Hydrolyzes Ppgpp And Functions In Starvation Responses
Nat. Struct. Mol. Biol. V. 17 1188 2010
PubMed-ID: 20818390 | Reference-DOI: 10.1038/NSMB.1906

Molecule 1 - HD DOMAIN-CONTAINING PROTEIN 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28(A)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HDDC3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	METAZOAN SPOT HOMOLOG 1, MESH1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:35 , HIS A:61 , ASP A:62 , ASP A:122 , HOH A:304	BINDING SITE FOR RESIDUE MN A 199
2	AC2	SOFTWARE	HIS B:35 , HIS B:61 , ASP B:62 , ASP B:122 , HOH B:275	BINDING SITE FOR RESIDUE MN B 199

(no "SS Bond" information available for 3NR1)

(no "Cis Peptide Bond" information available for 3NR1)

(no "SAP(SNP)/Variant" information available for 3NR1)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HD	PS51831	HD domain profile.	MESH1_HUMAN	32-127	2	A:32-127 B:32-127

(no "Exon" information available for 3NR1)

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
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Chain A from PDB  Type:PROTEIN  Length:178
 aligned with MESH1_HUMAN | Q8N4P3 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
          MESH1_HUMAN     2 GSEAAQLLEAADFAARKHRQQRRKDPEGTPYINHPIGVARILTHEAGITDIVVLQAALLHDTVEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLERKRLQVEQAPHSSPGAKLVKLADKLYNLRDLNRCTPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEEALKHLFKQRGLTI 179
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------HD  PDB: A:32-127 UniProt: 32-127                                                               ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nr1 A   2 GSEAAQLLEAADFAARKHRQQRRKDPEGTPYINHPIGVARILTHEAGITDIVVLQAALLHDTVEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLERKRLQVEQAPHSSPGAKLVKLADKLYNLRDLNRCTPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEEALKHLFKQRGLTI 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with MESH1_HUMAN | Q8N4P3 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
          MESH1_HUMAN     2 GSEAAQLLEAADFAARKHRQQRRKDPEGTPYINHPIGVARILTHEAGITDIVVLQAALLHDTVEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLERKRLQVEQAPHSSPGAKLVKLADKLYNLRDLNRCTPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEEALKHLFKQRGLTI 179
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------HD_4-3nr1B01 B:11-165                                                                                                                                      -------------- Pfam domains (1)
           Pfam domains (2) ---------HD_4-3nr1B02 B:11-165                                                                                                                                      -------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------HD  PDB: B:32-127 UniProt: 32-127                                                               ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nr1 B   2 GSEAAQLLEAADFAARKHRQQRRKDPEGTPYINHPIGVARILTHEAGITDIVVLQAALLHDTVEDTDTTLDEVELHFGAQVRRLVEEVTDDKTLPKLERKRLQVEQAPHSSPGAKLVKLADKLYNLRDLNRCTPEGWSEHRVQEYFEWAAQVVKGLQGTNRQLEEALKHLFKQRGLTI 179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

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 3NR1)

(no "CATH Domain" information available for 3NR1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HD_PDEase (93)

Family: HD_4 (1)

Homo sapiens (Human) (1)

1a	HD_4-3nr1B01	B:11-165
1b	HD_4-3nr1B02	B:11-165

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MESH1_HUMAN | Q8N4P3)

molecular function
	GO:0008728	GTP diphosphokinase activity	Catalysis of the reaction: ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
	GO:0008893	guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity	Catalysis of the reaction: guanosine 3',5'-bis(diphosphate) + H2O = guanosine 5'-diphosphate + diphosphate.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0015969	guanosine tetraphosphate metabolic process	The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates.
	GO:0042594	response to starvation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 3nr1)

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	3nr1
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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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