3U53 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN AP4A HYDROLASE

Authors :   H. H. Ge, M. K. Teng

Date :   10 Oct 11 (Deposition) - 10 Oct 12 (Release) - 20 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

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

Keywords :   Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. H. Ge, X. F. Chen, W. L. Yang, L. W. Niu, M. K. Teng
Crystal Structure Of Wild-Type And Mutant Human Ap4A Hydrolase
Biochem. Biophys. Res. Commun. V. 432 16 2013
PubMed-ID: 23384440 | Reference-DOI: 10.1016/J.BBRC.2013.01.095

Molecule 1 - BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE [ASYMMETRICAL]
	Chains	:	A, B, C, D
	EC Number	:	3.6.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NUDT2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ASYMMETRICAL DIADENOSINE TETRAPHOSPHATE HYDROLASE, AP4A HYDROLASE, AP4AASE, NUDIX HYDROLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 18)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	17	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 4 (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:22 , ALA A:23 , ILE A:24 , HIS A:139 , HOH A:175	BINDING SITE FOR RESIDUE SO4 A 156
02	AC2	SOFTWARE	HIS A:37 , LYS A:42 , TYR A:82 , ALA A:84	BINDING SITE FOR RESIDUE SO4 A 157
03	AC3	SOFTWARE	HIS A:109	BINDING SITE FOR RESIDUE SO4 A 158
04	AC4	SOFTWARE	ARG A:12 , ARG A:13 , VAL A:98 , LYS A:99 , TYR A:101	BINDING SITE FOR RESIDUE GOL A 159
05	AC5	SOFTWARE	ASN B:22 , ALA B:23 , ILE B:24 , HIS B:139 , HOH B:174 , HOH B:190	BINDING SITE FOR RESIDUE SO4 B 156
06	AC6	SOFTWARE	LEU B:70 , THR B:71 , ILE B:72 , LEU C:70 , ILE C:72	BINDING SITE FOR RESIDUE SO4 B 157
07	AC7	SOFTWARE	HIS B:44 , GLU B:58 , GLU B:110	BINDING SITE FOR RESIDUE SO4 B 158
08	AC8	SOFTWARE	HIS B:37 , LYS B:42 , TYR B:82 , ALA B:84	BINDING SITE FOR RESIDUE SO4 B 159
09	AC9	SOFTWARE	ARG A:12 , TYR C:114 , TRP C:116 , HOH C:173	BINDING SITE FOR RESIDUE SO4 C 156
10	BC1	SOFTWARE	ASN C:22 , ALA C:23 , ILE C:24 , HIS C:139 , HOH C:176	BINDING SITE FOR RESIDUE SO4 C 157
11	BC2	SOFTWARE	ASP C:100 , TYR C:101 , ASP C:102 , SO4 C:160 , HOH C:178	BINDING SITE FOR RESIDUE SO4 C 158
12	BC3	SOFTWARE	HIS C:37 , TYR C:82 , ALA C:84	BINDING SITE FOR RESIDUE SO4 C 159
13	BC4	SOFTWARE	ARG C:12 , ARG C:13 , GLU C:97 , VAL C:98 , LYS C:99 , SO4 C:158	BINDING SITE FOR RESIDUE SO4 C 160
14	BC5	SOFTWARE	ARG B:12 , TRP B:116 , TYR D:114 , TRP D:116 , HOH D:177 , HOH D:182	BINDING SITE FOR RESIDUE SO4 D 156
15	BC6	SOFTWARE	ASN D:22 , ALA D:23 , ILE D:24 , HIS D:139	BINDING SITE FOR RESIDUE SO4 D 157
16	BC7	SOFTWARE	LEU A:70 , THR A:71 , ILE A:72 , LEU D:70 , THR D:71 , ILE D:72	BINDING SITE FOR RESIDUE SO4 D 158
17	BC8	SOFTWARE	ARG B:115 , ASP D:100 , TYR D:101 , ASP D:102	BINDING SITE FOR RESIDUE SO4 D 159
18	BC9	SOFTWARE	LYS D:42 , TYR D:82 , ALA D:84	BINDING SITE FOR RESIDUE SO4 D 160

(no "SS Bond" information available for 3U53)

(no "Cis Peptide Bond" information available for 3U53)

(no "SAP(SNP)/Variant" information available for 3U53)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX_BOX	PS00893	Nudix box signature.	AP4A_HUMAN	43-64	4	A:43-64 B:43-64 C:43-64 D:43-64

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX_BOX	PS00893	Nudix box signature.	AP4A_HUMAN	43-64	1	A:43-64 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX_BOX	PS00893	Nudix box signature.	AP4A_HUMAN	43-64	1	- B:43-64 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX_BOX	PS00893	Nudix box signature.	AP4A_HUMAN	43-64	1	- - C:43-64 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX_BOX	PS00893	Nudix box signature.	AP4A_HUMAN	43-64	1	- - - D:43-64

Asymmetric Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000379158	1	ENSE00001357806	chr9:34329504-34329597	94	AP4A_HUMAN	-	0	0	-	-
1.3a	ENST00000379158	3a	ENSE00001479918	chr9:34336226-34336339	114	AP4A_HUMAN	-	0	0	-	-
1.4b	ENST00000379158	4b	ENSE00001357794	chr9:34338711-34338845	135	AP4A_HUMAN	-	0	0	-	-
1.5a	ENST00000379158	5a	ENSE00001089099	chr9:34339022-34339164	143	AP4A_HUMAN	1-43	43	4	A:4-43 B:4-43 C:4-43 D:4-43	40 40 40 40
1.6c	ENST00000379158	6c	ENSE00001479910	chr9:34343122-34343709	588	AP4A_HUMAN	43-147	105	4	A:43-147 B:43-147 C:43-147 D:43-147	105 105 105 105

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:144
 aligned with AP4A_HUMAN | P50583 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143    
           AP4A_HUMAN     4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
               SCOP domains d3u53a_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeeeeeeeeeeee..eeeeeeeeeeee............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------NUDIX_BOX  PDB: A:43-6----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: A:4-43 UniProt: 1-43    -------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.6c  PDB: A:43-147 UniProt: 43-147                                                                  Transcript 1 (2)
                 3u53 A   4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with AP4A_HUMAN | P50583 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143    
           AP4A_HUMAN     4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
               SCOP domains d3u53b_ B: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeeeeeeeeeeee..eeeeeeeeeeee............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------NUDIX_BOX  PDB: B:43-6----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: B:4-43 UniProt: 1-43    -------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.6c  PDB: B:43-147 UniProt: 43-147                                                                  Transcript 1 (2)
                 3u53 B   4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain C from PDB  Type:PROTEIN  Length:144
 aligned with AP4A_HUMAN | P50583 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143    
           AP4A_HUMAN     4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
               SCOP domains d3u53c_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eee.....eeeeeee..eeeeeeeeeeee............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------NUDIX_BOX  PDB: C:43-6----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: C:4-43 UniProt: 1-43    -------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.6c  PDB: C:43-147 UniProt: 43-147                                                                  Transcript 1 (2)
                 3u53 C   4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with AP4A_HUMAN | P50583 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143    
           AP4A_HUMAN     4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
               SCOP domains d3u53d_ D: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eee.....eeeeeee..eeeeeeeeeeee............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------NUDIX_BOX  PDB: D:43-6----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: D:4-43 UniProt: 1-43    -------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.6c  PDB: D:43-147 UniProt: 43-147                                                                  Transcript 1 (2)
                 3u53 D   4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRETQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEA 147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: MutT-like (82)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d3u53a_	A:
1b	d3u53b_	B:
1c	d3u53c_	C:
1d	d3u53d_	D:

(no "CATH Domain" information available for 3U53)

(no "Pfam Domain" information available for 3U53)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AP4A_HUMAN | P50583)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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:0008803	bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity	Catalysis of the reaction: P(1),P(4)-bis(5'-adenosyl) tetraphosphate + H(2)O = 2 ADP + 2 H(+).
	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.
	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: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:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0000302	response to reactive oxygen species	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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	Cis Peptide Bonds
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	3u53
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	AP4A_HUMAN \| P50583	:	1xsa 1xsb 1xsc 4ick 4ijx

(no "Related Entries Specified in the PDB File" available for 3U53)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (2, 8)

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