3HYF - JenaLib

Title :   CRYSTAL STRUCTURE OF HIV-1 RNASE H P15 WITH ENGINEERED E. COLI LOOP AND ACTIVE SITE INHIBITOR

Authors :   E. B. Lansdon, T. A. Kirschberg

Date :   22 Jun 09 (Deposition) - 20 Oct 09 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Rnase H, Hiv-1, Hydrolase, Di-Valent Metal Nucleic Acid Cleavage Mechanism, Di-Valent Metal Coordination, Aspartyl Protease, Dna Integration, Dna Recombination, Endonuclease, Multifunctional Enzyme, Nuclease, Nucleotidyltransferase, Protease, Rna-Directed Dna Polymerase, Transferase, Magnesium, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Kirschberg, M. Balakrishnan, N. H. Squires, T. Barnes, K. M. Brendza, X. Chen, E. J. Eisenberg, W. Jin, N. Kutty, S. Leavitt, A. Liclican, Q. Liu, X. Liu, J. Mak, J. K. Perry, M. Wang, W. J. Watkins, E. B. Lansdon
Rnase H Active Site Inhibitors Of Human Immunodeficiency Virus Type 1 Reverse Transcriptase: Design, Biochemical Activity, And Structural Information.
J. Med. Chem. V. 52 5781 2009
PubMed-ID: 19791799 | Reference-DOI: 10.1021/JM900597Q

Compounds

Molecule 1 - REVERSE TRANSCRIPTASE/RNASEH
	Chains	:	A
	EC Number	:	3.1.26.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30B
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	POL, REVERSE TRANSCRIPTASE (AMINO ACIDS 427-560)
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1,ESCHERICHIA COLI
	Organism Taxid	:	11676,83333

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:443 , GLU A:478 , ASP A:498 , MN A:602 , ON1 A:701	BINDING SITE FOR RESIDUE MN A 601
2	AC2	SOFTWARE	ASP A:443 , ASP A:549 , MN A:601 , HOH A:603 , HOH A:604 , ON1 A:701	BINDING SITE FOR RESIDUE MN A 602
3	AC3	SOFTWARE	HOH A:166 , TYR A:441 , GLY A:544 , GLN A:547	BINDING SITE FOR RESIDUE ACT A 650
4	AC4	SOFTWARE	HOH A:10 , HOH A:33 , HOH A:180 , HOH A:184 , ARG A:461 , GLY A:490	BINDING SITE FOR RESIDUE GOL A 698
5	AC5	SOFTWARE	HOH A:182 , ARG A:448 , THR A:473 , ASN A:474 , GLN A:475	BINDING SITE FOR RESIDUE GOL A 699
6	AC6	SOFTWARE	HOH A:4 , HOH A:7 , HOH A:15 , HOH A:41 , ASP A:443 , GLU A:478 , ASP A:498 , GLN A:500 , ALA A:538 , HIS A:539 , ASP A:549 , ARG A:557 , MN A:601 , MN A:602 , HOH A:603 , HOH A:604	BINDING SITE FOR RESIDUE ON1 A 701

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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
	(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:143
 aligned with Q72547_9HIV1 | Q72547 from UniProtKB/TrEMBL  Length:566

    Alignment length:144
                                                                                                          506       507                                                     
                                   435       445       455       465       475       485       495       505|        -|      516       526       536       546       556    
         Q72547_9HIV1   426 WYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGII---------QAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL 560
               SCOP domains d3hyfa_ A: automated matches                                                                                                                     SCOP domains
               CATH domains 3hyfA00 A:426-560  [code=3.30.420.10, no name defined]                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeeeee......eeeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh.....hhh-hhhhhhhhhh...eeeeee......hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hyf A 426 MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVD-LVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVL 560
                                   435       445       455       465       475       485       495       505||      87  ||    |-|      526       536       546       556    
                                                                                                          506|         90|  102 |                                           
                                                                                                            79          97    517

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (17, 21)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q72547_9HIV1 | Q72547)

molecular function
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0003964	RNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
	GO:0006278	RNA-dependent DNA biosynthetic process	A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.

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Description