1KTG - JenaLib

Title :   CRYSTAL STRUCTURE OF A C. ELEGANS AP4A HYDROLASE BINARY COMPLEX

Authors :   S. Bailey, S. E. Sedelnikova, G. M. Blackburn, H. M. Abdelghany, P. J. Baker, A. G. Mclennan, J. B. Rafferty

Date :   16 Jan 02 (Deposition) - 08 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Nudix, Amp, Magnesium Cluster, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bailey, S. E. Sedelnikova, G. M. Blackburn, H. M. Abdelghany, P. J. Baker, A. G. Mclennan, J. B. Rafferty
The Crystal Structure Of Diadenosine Tetraphosphate Hydrolase From Caenorhabditis Elegans In Free And Binary Complex Forms
Structure V. 10 589 2002
PubMed-ID: 11937063 | Reference-DOI: 10.1016/S0969-2126(02)00746-3
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:36 , GLY A:37 , HIS A:38 , GLU A:52 , GLU A:56 , GLU A:103 , MG A:502 , MG A:503 , MG A:504 , MG A:505 , OH A:506 , HOH A:715 , HOH A:722 , HOH A:732 , HOH A:749 , HOH A:756 , HOH A:769 , HOH A:827	BINDING SITE FOR RESIDUE PO4 A 402
02	AC2	SOFTWARE	LYS B:36 , GLY B:37 , HIS B:38 , GLU B:52 , GLU B:56 , GLU B:103 , MG B:601 , MG B:602 , MG B:603 , MG B:604 , OH B:605 , HOH B:615 , HOH B:631 , HOH B:635 , HOH B:654 , HOH B:669 , HOH B:672 , HOH B:703	BINDING SITE FOR RESIDUE PO4 B 401
03	AC3	SOFTWARE	GLU A:52 , GLU A:103 , PO4 A:402 , MG A:503 , MG A:504 , MG A:505 , HOH A:708 , HOH A:742 , HOH A:752 , HOH A:756	BINDING SITE FOR RESIDUE OH A 506
04	AC4	SOFTWARE	GLU B:52 , GLU B:103 , PO4 B:401 , MG B:601 , MG B:603 , MG B:604 , HOH B:611 , HOH B:633 , HOH B:650 , HOH B:654	BINDING SITE FOR RESIDUE OH B 605
05	AC5	SOFTWARE	GLU A:19 , GLU A:111 , HOH A:729 , HOH A:737 , HOH B:616 , HOH B:638 , HOH B:644	BINDING SITE FOR RESIDUE MG A 501
06	AC6	SOFTWARE	LYS A:36 , GLU A:56 , PO4 A:402 , MG A:505 , HOH A:722 , HOH A:732 , HOH A:734	BINDING SITE FOR RESIDUE MG A 502
07	AC7	SOFTWARE	GLU A:52 , PO4 A:402 , MG A:504 , MG A:505 , OH A:506 , HOH A:715 , HOH A:752 , HOH A:756	BINDING SITE FOR RESIDUE MG A 503
08	AC8	SOFTWARE	GLU A:103 , PO4 A:402 , MG A:503 , MG A:505 , OH A:506 , HOH A:742 , HOH A:749 , HOH A:756	BINDING SITE FOR RESIDUE MG A 504
09	AC9	SOFTWARE	GLU A:52 , GLU A:56 , GLU A:103 , PO4 A:402 , MG A:502 , MG A:503 , MG A:504 , OH A:506 , HOH A:708	BINDING SITE FOR RESIDUE MG A 505
10	BC1	SOFTWARE	GLU B:103 , PO4 B:401 , MG B:603 , MG B:604 , OH B:605 , HOH B:611 , HOH B:654 , HOH B:672	BINDING SITE FOR RESIDUE MG B 601
11	BC2	SOFTWARE	LYS B:36 , GLU B:56 , PO4 B:401 , MG B:603 , HOH B:607 , HOH B:615 , HOH B:669	BINDING SITE FOR RESIDUE MG B 602
12	BC3	SOFTWARE	GLU B:52 , GLU B:56 , GLU B:103 , PO4 B:401 , MG B:601 , MG B:602 , MG B:604 , OH B:605 , HOH B:650	BINDING SITE FOR RESIDUE MG B 603
13	BC4	SOFTWARE	GLU B:52 , PO4 B:401 , MG B:601 , MG B:603 , OH B:605 , HOH B:633 , HOH B:635 , HOH B:654	BINDING SITE FOR RESIDUE MG B 604
14	BC5	SOFTWARE	PRO A:29 , HIS A:31 , LYS A:36 , TYR A:76 , LYS A:83 , TYR A:121 , HOH A:782 , HOH A:843	BINDING SITE FOR RESIDUE AMP A 701

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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:137
 aligned with AP4A_CAEEL | Q9U2M7 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
           AP4A_CAEEL     2 VVKAAGLVIYRKLAGKIEFLLLQASYPPHHWTPPKGHVDPGEDEWQAAIRETKEEANITKEQLTIHEDCHETLFYEAKGKPKSVKYWLAKLNNPDDVQLSHEHQNWKWCELEDAIKIADYAEMGSLLRKFSAFLAGF 138
               SCOP domains d1ktga_ A: Diadenosine tetraphosphate hydrolase (Ap4A hydrolase)                                                                          SCOP domains
               CATH domains 1ktgA00 A:2-138 Nucleoside Triphosphate Pyrophosphohydrolase                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeeeeeeeeeeee..eeeeeeeeeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------NUDIX_BOX  PDB: A:37-5-------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktg A   2 VVKAAGLVIYRKLAGKIEFLLLQASYPPHHWTPPKGHVDPGEDEWQAAIRETKEEANITKEQLTIHEDCHETLFYEAKGKPKSVKYWLAKLNNPDDVQLSHEHQNWKWCELEDAIKIADYAEMGSLLRKFSAFLAGF 138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with AP4A_CAEEL | Q9U2M7 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:135
                                    13        23        33        43        53        63        73        83        93       103       113       123       133     
           AP4A_CAEEL     4 KAAGLVIYRKLAGKIEFLLLQASYPPHHWTPPKGHVDPGEDEWQAAIRETKEEANITKEQLTIHEDCHETLFYEAKGKPKSVKYWLAKLNNPDDVQLSHEHQNWKWCELEDAIKIADYAEMGSLLRKFSAFLAGF 138
               SCOP domains d1ktgb_ B: Diadenosine tetraphosphate hydrolase (Ap4A hydrolase)                                                                        SCOP domains
               CATH domains 1ktgB00 B:4-138 Nucleoside Triphosphate Pyrophosphohydrolase                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee......eeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeeeeeeeeee..---.eeeeeeeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------NUDIX_BOX  PDB: B:37-5-------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktg B   4 KAAGLVIYRKLAGKIEFLLLQASYPPHHWTPPKGHVDPGEDEWQAAIRETKEEANITKEQLTIHEDCHETLFYEA---PKSVKYWLAKLNNPDDVQLSHEHQNWKWCELEDAIKIADYAEMGSLLRKFSAFLAGF 138
                                    13        23        33        43        53        63        73    |   83        93       103       113       123       133     
                                                                                                     78  82

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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AP4A_CAEEL | Q9U2M7)

molecular function
	GO:0043135	5-phosphoribosyl 1-pyrophosphate pyrophosphatase activity	Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + H2O = ribose 1,5 bisphosphate + phosphate + H+.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004081	bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity	Catalysis of the reaction: P(1),P(4)-bis(5'-nucleosyl)tetraphosphate + H2O = NTP + NMP. Acts on bis(5'-guanosyl)-, bis(5'-xanthosyl)-, bis(5'-adenosyl)- and bis(5'-uridyl)-tetraphosphate.
	GO:0008796	bis(5'-nucleosyl)-tetraphosphatase activity	Catalysis of the hydrolysis of P(1),P(4)-bis(5'-nucleosyl)tetraphosphate into two nucleotides.
	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.
biological process
	GO:0006172	ADP biosynthetic process	The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
	GO:0006167	AMP biosynthetic process	The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
	GO:0006754	ATP biosynthetic process	The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0015967	diadenosine tetraphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of diadenosine tetraphosphate, a derivative of the nucleoside adenosine with four phosphate groups attached.
	GO:0019693	ribose phosphate metabolic process	The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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