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Description

Title :   CRYSTAL STRUCTURE OF A HISTIDINE TRIAD FAMILY PROTEIN FROM ENTAMOEBA HISTOLYTICA, BOUND TO AMP

Authors :   Ssgcid, Seattle Structural Genomics Center For Infectious Dis (Ssgcid)

Date :   26 Aug 10 (Deposition) - 08 Sep 10 (Release) - 20 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Ssgcid, Putative Hydrolase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. D. Lorimer, R. Choi, A. Abramov, S. Nakazawa Hewitt, A. S. Gardberg W. C. Van Voorhis, B. L. Staker, P. J. Myler, T. E. Edwards
Structures Of A Histidine Triad Family Protein From Entamoeba Histolytica Bound To Sulfate, Amp And Gmp.
Acta Crystallogr F Struct V. 71 572 2015 Biol Commun
PubMed-ID: 25945711 | Reference-DOI: 10.1107/S2053230X1500237X

Compounds

Molecule 1 - PUTATIVE HISTIDINE TRIAD FAMILY PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	EHI_093910
	Organism Scientific	:	ENTAMOEBA HISTOLYTICA
	Organism Taxid	:	294381

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:5 , CYS A:8 , HIS A:47 , HIS A:97	BINDING SITE FOR RESIDUE ZN A 114
2	AC2	SOFTWARE	PHE A:29 , LYS A:30 , ASP A:31 , ILE A:32 , ASN A:33 , LEU A:41 , ASN A:86 , GLY A:92 , GLN A:93 , THR A:94 , HIS A:99 , HIS A:101 , HOH A:150 , HOH A:199 , HOH A:205 , HOH A:223 , HOH A:262 , HOH A:271	BINDING SITE FOR RESIDUE AMP A 115

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HIT_ENTHI	6-113	1	A:6-113
2	HIT_1	PS00892	HIT domain signature.	HIT_ENTHI	86-104	1	A:86-104

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HIT_ENTHI	6-113	2	A:6-113
2	HIT_1	PS00892	HIT domain signature.	HIT_ENTHI	86-104	2	A:86-104

Exons (0, 0)

(no "Exon" information available for 3OMF)

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)
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Chain A from PDB  Type:PROTEIN  Length:111
 aligned with HIT_ENTHI | C4LYI2 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:111
                                    12        22        32        42        52        62        72        82        92       102       112 
            HIT_ENTHI     3 DSCIFCKIAQKQIPSTIVYEDDEIFAFKDINPIAPIHILVIPKQHIASLNEITEENEAFIGKVLYKVSLIGKKECPEGYRVVNNIGEDAGQTVKHIHFHILGGKKLAWDKL 113
               SCOP domains d3omfa_ A: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh......eeee...eeeee.......eeeeeee.....hhhhh...hhhhhhhhhhhhhhhhhhhh...eeee...............eeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: A:6-113 UniProt: 6-113                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------HIT_1  PDB: A:86-10--------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 3omf A   3 DSCIFCKIAQKQIPSTIVYEDDEIFAFKDINPIAPIHILVIPKQHIASLNEITEENEAFIGKVLYKVSLIGKKECPEGYRVVNNIGEDAGQTVKHIHFHILGGKKLAWDKL 113
                                    12        22        32        42        52        62        72        82        92       102       112

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: HIT-like (73)

Superfamily: HIT-like (67)

Family: automated matches (11)

Protein domain: automated matches (11)

Entamoeba histolytica [TaxId: 294381] (3)

d3omfa_

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (HIT_ENTHI | C4LYI2)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	HIT_ENTHI \| C4LYI2	:	3oj7 3oxk

Related Entries Specified in the PDB File

3oj7	STRUCTURE OF THE SAME HIT PROTEIN BOUND TO SULFATE RELATED ID: ENHIA.01296.A RELATED DB: TARGETDB
3oxk	STRUCTURE OF THE SAME PROTEIN BOUND TO GMP