3CR7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF N-TERMINAL TRUNCATION OF APS KINASE FROM PENICILLIUM CHRYSOGENUM: TERNARY STRUCTURE WITH ADP AND PAPS

Authors :   S. C. Gay, I. H. Segel, A. J. Fisher

Date :   04 Apr 08 (Deposition) - 17 Feb 09 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Aps Kinase, Adenylylsulfate Kinase, Transferase, Sulfate Metabolism, Nucleotide 2 Kinase, Amino-Acid Biosynthesis, Atp-Binding, Cysteine Biosynthesis, Methionine Biosynthesis, Nucleotide-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Gay, I. H. Segel, A. J. Fisher
Truncated Aps Kinase From Pencillium Chrysogenum: Insight Into The Function Of The N-Terminal Helix
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ADENYLYL-SULFATE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 23-211
	Organism Common	:	PENICILLIUM NOTATUM
	Organism Scientific	:	PENICILLIUM CHRYSOGENUM
	Organism Taxid	:	5076
	Strain	:	ATTC 24791
	Synonym	:	APS KINASE, ADENOSINE-5'-PHOSPHOSULFATE KINASE, ATP ADENOSINE-5'-PHOSPHOSULFATE 3'-PHOSPHOTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	PPS	2	Ligand/Ion	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PPS	1	Ligand/Ion	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	PPS	1	Ligand/Ion	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:156 , HOH A:2038 , TYR D:172	BINDING SITE FOR RESIDUE CL A 503
2	AC2	SOFTWARE	SER B:107	BINDING SITE FOR RESIDUE CL B 502
3	AC3	SOFTWARE	TYR B:172 , LYS C:156	BINDING SITE FOR RESIDUE CL C 501
4	AC4	SOFTWARE	SER A:34 , ALA A:35 , SER A:36 , GLY A:37 , LYS A:38 , SER A:39 , THR A:40 , ARG A:148 , PRO A:150 , LEU A:187 , HOH A:2052 , HOH A:2085 , HOH A:2098 , GLU C:186	BINDING SITE FOR RESIDUE ADP A 2001
5	AC5	SOFTWARE	ARG A:66 , PHE A:75 , ARG A:80 , ASN A:83 , PHE A:105 , ILE A:106 , SER A:107 , PRO A:108 , LYS A:151 , LEU A:153 , ILE A:162 , LYS A:163 , GLU A:164 , PHE A:165 , THR A:166 , HOH A:2018 , HOH A:2042 , HOH A:2098 , HOH A:2109	BINDING SITE FOR RESIDUE PPS A 2002
6	AC6	SOFTWARE	SER B:34 , ALA B:35 , SER B:36 , GLY B:37 , LYS B:38 , SER B:39 , THR B:40 , ARG B:148 , PRO B:150 , ASN B:184 , LEU B:187 , VAL B:189 , HOH B:2004 , HOH B:2119 , ARG D:148 , ADP D:2006 , HOH D:2111	BINDING SITE FOR RESIDUE ADP B 2003
7	AC7	SOFTWARE	GLU A:186 , SER C:34 , ALA C:35 , SER C:36 , GLY C:37 , LYS C:38 , SER C:39 , THR C:40 , ARG C:148 , PRO C:150 , LYS C:151 , ASN C:184 , LEU C:187 , HOH C:2086	BINDING SITE FOR RESIDUE ADP C 2004
8	AC8	SOFTWARE	ARG C:66 , PHE C:75 , ARG C:80 , ASN C:83 , ILE C:84 , PHE C:105 , ILE C:106 , SER C:107 , PRO C:108 , LEU C:153 , LYS C:163 , GLU C:164 , PHE C:165 , THR C:166	BINDING SITE FOR RESIDUE PPS C 2005
9	AC9	SOFTWARE	ARG B:148 , ADP B:2003 , HOH B:2004 , LEU D:33 , ALA D:35 , SER D:36 , GLY D:37 , LYS D:38 , SER D:39 , THR D:40 , ARG D:148 , ASN D:184 , LEU D:187 , HOH D:2010 , HOH D:2012 , HOH D:2039 , HOH D:2111	BINDING SITE FOR RESIDUE ADP D 2006

(no "SS Bond" information available for 3CR7)

(no "Cis Peptide Bond" information available for 3CR7)

(no "SAP(SNP)/Variant" information available for 3CR7)

(no "PROSITE Motif" information available for 3CR7)

(no "Exon" information available for 3CR7)

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:179
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:185
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     
           KAPS_PENCH    24 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPA 208
               SCOP domains d3cr7a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhh......eeeehhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh------....eeeeeee.hhhhhhhhh..hhhhhhhh....................eeee....hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cr7 A  24 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEV------TGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPA 208
                                    33        43        53        63        73        83        93       103       113        |-     | 133       143       153       163       173       183       193       203     
                                                                                                                            122    129

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:186
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203      
           KAPS_PENCH    24 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
               SCOP domains d3cr7b_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh...eeeehhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhh.-----.....eeeeeee.hhhhhhhhh..hhhhhhhhh...................eeee....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cr7 B  24 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEV-----ETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPAK 209
                                    33        43        53        63        73        83        93       103       113        |-    |  133       143       153       163       173       183       193       203      
                                                                                                                            122   128

Chain C from PDB  Type:PROTEIN  Length:178
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:184
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202    
           KAPS_PENCH    23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYL 206
               SCOP domains d3cr7c_ C: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhh...........hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh------....eeeeeee.hhhhhhhhh..hhhhhhhhh...................eeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cr7 C  23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEV------TGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYL 206
                                    32        42        52        62        72        82        92       102       112       122      |132       142       152       162       172       182       192       202    
                                                                                                                             122    129

Chain D from PDB  Type:PROTEIN  Length:183
 aligned with KAPS_PENCH | Q12657 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:186
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      
           KAPS_PENCH    23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPA 208
               SCOP domains d3cr7d_ D: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhh....eeeehhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh---......eeeeeee.hhhhhhhhh..hhhhhhhhh...................eeee....hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cr7 D  23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFADSNSIAITSFISPYRKDRDTARQLHEVA---EETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKNYELPVQDAVKQIIDYLDTKGYLPA 208
                                    32        42        52        62        72        82        92       102       112       122|   |  132       142       152       162       172       182       192       202      
                                                                                                                              123 127

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 "CATH Domain" information available for 3CR7)

(no "Pfam Domain" information available for 3CR7)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (KAPS_PENCH | Q12657)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0098617	adenylylselenate kinase activity	Catalysis of the reaction: ATP + Adenylylselenate => ADP + 3'-Phosphoadenylylselenate.
	GO:0004020	adenylylsulfate kinase activity	Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019344	cysteine biosynthetic process	The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0070814	hydrogen sulfide biosynthetic process	The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PPS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3cr7)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3cr7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	KAPS_PENCH \| Q12657
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.25
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	KAPS_PENCH \| Q12657
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	KAPS_PENCH \| Q12657	:	1d6j 1m7g 1m7h

1d6j	FULL LENGTH STRUCUTRE, APO
1m7g	FULL LENGTH PROTEIN IN COMPLEX WITH ADP AND APS
1m7h	FULL LENGTH PROTEIN IN COMPLEX WITH ADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

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

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File