3KTA - JenaLib

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Title :   STRUCTURAL BASIS FOR ADENYLATE KINASE ACTIVITY IN ABC ATPASES

Authors :   A. Lammens, K. P. Hopfner

Date :   24 Nov 09 (Deposition) - 30 Jun 10 (Release) - 11 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Structural Maintenance Of Chromosomes, Smc, Abc Atpase, Cftr, Adenylate Kinase, Ap5A, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Lammens, K. P. Hopfner
Structural Basis For Adenylate Kinase Activity In Abc Atpases.
J. Mol. Biol. V. 401 265 2010
PubMed-ID: 20600125 | Reference-DOI: 10.1016/J.JMB.2010.06.029

Molecule 1 - CHROMOSOME SEGREGATION PROTEIN SMC
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 115-296
	Gene	:	PF1843
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

Molecule 2 - CHROMOSOME SEGREGATION PROTEIN SMC
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1120-1291
	Gene	:	PF1843
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

		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, 22)

No.	Name	Count	Type	Full Name
1	AP5	2	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	AP5	1	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	AP5	1	Ligand/Ion	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:13 , SER A:14 , ASN A:35 , GLY A:36 , SER A:37 , GLY A:38 , LYS A:39 , SER A:40 , ASN A:41 , ARG A:59 , ASP A:65 , ILE A:67 , PHE A:68 , ALA A:69 , GLN A:145 , MG A:184 , HOH A:186 , HOH A:187 , HOH A:194 , HOH A:196 , HOH A:202 , HOH A:230 , HOH A:235 , HOH A:237 , HOH A:238 , HOH A:239 , HOH A:252 , HOH A:318 , HOH A:351 , HOH A:353 , HOH A:517 , HOH A:607 , HOH B:2 , GLU B:1098 , HIS B:1175 , GLY B:1176 , ASN B:1177 , GLY C:146 , THR C:149 , LYS C:153 , HOH D:374 , ARG D:1065 , GLU D:1067 , LYS D:1074	BINDING SITE FOR RESIDUE AP5 A 183
2	AC2	SOFTWARE	SER A:40 , GLN A:145 , AP5 A:183 , HOH A:186 , HOH B:2	BINDING SITE FOR RESIDUE MG A 184
3	AC3	SOFTWARE	HOH B:671 , GLU B:1067 , ALA B:1068 , MSE B:1069 , HIS B:1102 , LEU B:1103 , ASP B:1104 , GLU B:1174 , LYS C:13 , SER C:14 , ALA C:34 , ASN C:35 , GLY C:36 , SER C:37 , GLY C:38 , LYS C:39 , SER C:40 , ASN C:41 , ARG C:59 , SER C:64 , ASP C:65 , ILE C:67 , PHE C:68 , ALA C:69 , GLN C:145 , MG C:184 , HOH C:185 , HOH C:247 , HOH C:356 , HOH C:363 , HOH C:515 , HOH C:522 , HOH C:689 , HOH C:843 , HOH C:844 , HOH D:3 , HOH D:357 , GLU D:1098	BINDING SITE FOR RESIDUE AP5 C 183
4	AC4	SOFTWARE	SER C:40 , GLN C:145 , AP5 C:183 , HOH C:185 , HOH D:3	BINDING SITE FOR RESIDUE MG C 184

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

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

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

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

(no "Exon" information available for 3KTA)

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:164
 aligned with SMC_PYRFU | Q8TZY2 from UniProtKB/Swiss-Prot  Length:1177

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           SMC_PYRFU      2 PYIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRASRISDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATRSEILDILTAAMISPDGYNIVLQGDITKFIKMSPLERRLLIDDISGI  169
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.hhhhh...eeee....eeeeee....hhhhhhhhhhhhh....hhhhh..hhhhhh....----....eeeeeeee...........eeeeeeee.....eeeee..eeehhhhhhhhhhhh........ee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3kta A    2 PYIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAmRASRISDLIFAGS----PAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATRSEILDILTAAmISPDGYNIVLQGDITKFIKmSPLERRLLIDDISGI  169
                                    11        21        31        41        51      | 61        71    |   81        91       101       111       121       131  |    141       151  |    161        
                                                                                   58-MSE       71   76                                                       134-MSE             154-MSE

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with SMC_PYRFU | Q8TZY2 from UniProtKB/Swiss-Prot  Length:1177

    Alignment length:171
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176 
           SMC_PYRFU   1007 KEKKNVFMRTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPAGKDVKRIEAMSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFIVITLRDVMMANADKIIGVSMRDGVSKVVSLSLEKAMKILEEIRKKQGWEHGN 1177
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhh.eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeeeeeee..eeeeee.hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3kta B 1007 KEKKNVFmRTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPAGKDVKRIEAmSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFIVITLRDVmmANADKIIGVSmRDGVSKVVSLSLEKAmKILEEIRKKQGWEHGN 1177
                                  1016      1026      1036      1046      1056      1066  |   1076      1086      1096      1106      1116      1126      1136      1146      1156    | 1166      1176 
                                1014-MSE                                               1069-MSE                                                        1133-MSE    1145-MSE        1161-MSE            
                                                                                                                                                        1134-MSE

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with SMC_PYRFU | Q8TZY2 from UniProtKB/Swiss-Prot  Length:1177

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           SMC_PYRFU      2 PYIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAMRASRISDLIFAGSKNEPPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATRSEILDILTAAMISPDGYNIVLQGDITKFIKMSPLERRLLIDDISGI  169
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.hhhhh...eeee....eeeeee....hhhhhhhhhhhhh...........hhhhh...-----.....eeeeeeee...........eeeeeeee.....eeeee..eeehhhhhhhhhhhh........ee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3kta C    2 PYIEKLELKGFKSYGNKKVVIPFSKGFTAIVGANGSGKSNIGDAILFVLGGLSAKAmRASRISDLIFA-----PPAKYAEVAIYFNNEDRGFPIDEDEVVIRRRVYPDGRSSYWLNGRRATRSEILDILTAAmISPDGYNIVLQGDITKFIKmSPLERRLLIDDISGI  169
                                    11        21        31        41        51      | 61       | -   |    81        91       101       111       121       131  |    141       151  |    161        
                                                                                   58-MSE     69    75                                                        134-MSE             154-MSE

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with SMC_PYRFU | Q8TZY2 from UniProtKB/Swiss-Prot  Length:1177

    Alignment length:162
                                  1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167  
           SMC_PYRFU   1008 EKKNVFMRTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPAGKDVKRIEAMSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFIVITLRDVMMANADKIIGVSMRDGVSKVVSLSLEKAMKILEEIRK 1169
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------SMC_N-3ktaD01 D:1120-1151       ------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------SMC_N-3ktaD02 D:1120-1151       ------------------ Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------SMC_N-3ktaD03 D:1120-1151       ------------------ Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------SMC_N-3ktaD04 D:1120-1151       ------------------ Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhh.eeeeee..----.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeeeeeee..eeeeee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3kta D 1008 EKKNVFmRTFEAISRNFSEIFAKLSPGGSARLILENPEDPFSGGLEIEAKPA----KRIEAmSGGEKALTALAFVFAIQKFKPAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFIVITLRDVmmANADKIIGVSmRDGVSKVVSLSLEKAmKILEEIRK 1169
                                  1017      1027      1037      1047      1057 |    1067 |    1077      1087      1097      1107      1117      1127     |1137      1147      1157   |  1167  
                               1014-MSE                                     1059 1064    |                                                            1133-MSE    1145-MSE        1161-MSE    
                                                                                      1069-MSE                                                         1134-MSE

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 "SCOP Domain" information available for 3KTA)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: SMC_N (5)

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (2)

1a	SMC_N-3ktaD01	D:1120-1151
1b	SMC_N-3ktaD02	D:1120-1151
1c	SMC_N-3ktaD03	D:1120-1151
1d	SMC_N-3ktaD04	D:1120-1151

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SMC_PYRFU | Q8TZY2)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0030261	chromosome condensation	The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
	GO:0051276	chromosome organization	A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
	GO:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0007062	sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	SMC_PYRFU \| Q8TZY2	:	1xew 1xex 3nwc 4i99 4rsj

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Description

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Ligands, Modified Residues, Ions (3, 22)

Sites (4, 4)

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