1R8J - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CIRCADIAN CLOCK PROTEIN KAIA FROM SYNECHOCOCCUS ELONGATUS

Authors :   S. Ye, I. Vakonakis, J. C. Sacchettini, A. C. Liwang

Date :   26 Oct 03 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

Chains :   Asym./Biol. Unit : A,B

Keywords :   Kaia, Circadian Clock Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ye, I. Vakonakis, T. R. Ioerger, A. C. Liwang, J. C. Sacchettini
Crystal Structure Of Circadian Clock Protein Kaia From Synechococcus Elongatus
J. Biol. Chem. V. 279 20511 2004
PubMed-ID: 15007067 | Reference-DOI: 10.1074/JBC.M400077200
(for further references see the PDB file header)

Molecule 1 - KAIA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET32A+
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	KAIA
	Organism Scientific	:	SYNECHOCOCCUS ELONGATUS PCC 7942
	Organism Taxid	:	1140
	Strain	:	PCC 7942

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1R8J)

(no "Site" information available for 1R8J)

(no "SS Bond" information available for 1R8J)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:129	-	Pro A:130
2	Ala B:129	-	Pro B:130

(no "SAP(SNP)/Variant" information available for 1R8J)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KAIA_N	PS51430	KaiA N-terminal domain profile.	KAIA_SYNE7	1-164	2	A:2-164 B:2-164
2	KAIA_C	PS51431	KaiA C-terminal domain profile.	KAIA_SYNE7	174-282	2	A:174-282 B:174-282

(no "Exon" information available for 1R8J)

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:272
 aligned with KAIA_SYNE7 | Q79PF6 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           KAIA_SYNE7     1 MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLMGANHDPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPR 282
               SCOP domains d1r8ja2 A:1-135 N-terminal domain of the circadian clock protein KaiA                                                                  ------    -------------------------------d1r8ja1 A:177-282 Circadian clock protein KaiA, C-terminal domain                                          SCOP domains
               CATH domains 1r8jA01 A:1-141,A:146-167  [code=3.40.50.2300, no name defined]                                                                                  1r8jA01               1r8jA02 A:168-282 KaiA/RbsU domain                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh.....eeee....------...........eee...hhhhhhhhhhhhhhhhhhhh............----..hhhhhhhhhhhhhhhhheeeeeee..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE KAIA_N  PDB: A:2-164 UniProt: 1-164                                                                                                                                 ---------KAIA_C  PDB: A:174-282 UniProt: 174-282                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r8j A   1 VLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRD------PAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLM----DPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPR 282
                                    10        20        30        40        50        60        70        80     |   -  |    100       110       120       130       140|    | 150       160       170       180       190       200       210       220       230       240       250       260       270       280  
                                                                                                                86     93                                             141  146

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with KAIA_SYNE7 | Q79PF6 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           KAIA_SYNE7     1 MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLMGANHDPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPR 282
               SCOP domains d1r8jb2 B:1-135 N-terminal domain of the circadian clock protein KaiA                                                                  -          ------------------------------d1r8jb1 B:177-282 Circadian clock protein KaiA, C-terminal domain                                          SCOP domains
               CATH domains 1r8jB01 B:1-136,B:147-167  [code=3.40.50.2300, no name defined]                                                                                   1r8jB01              1r8jB02 B:168-282 KaiA/RbsU domain                                                                                  CATH domains
           Pfam domains (1) ----KaiA-1r8jB01 B:5-282                                                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) ----KaiA-1r8jB02 B:5-282                                                                                                                                                                                                                                                                   Pfam domains (2)
         Sec.struct. author ....eeeeee..hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh.....eeee..--------...........eee......hhhhhhhhhhhhhhhhh.......----------....hhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE KAIA_N  PDB: B:2-164 UniProt: 1-164                                                                                                                                 ---------KAIA_C  PDB: B:174-282 UniProt: 174-282                                                                       PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r8j B   1 VLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGD--------PAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMAD----------PELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPR 282
                                    10        20        30        40        50        60        70        80   |     -  |    100       110       120       130     |   -      |150       160       170       180       190       200       210       220       230       240       250       260       270       280  
                                                                                                              84       93                                        136        147

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: KaiA] (7)

Family: KaiA (7)

Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2) (3)

1a	KaiA-1r8jB01	B:5-282
1b	KaiA-1r8jB02	B:5-282

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KAIA_SYNE7 | Q79PF6)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0009649	entrainment of circadian clock	The synchronization of a circadian rhythm to environmental time cues such as light.
	GO:0035308	negative regulation of protein dephosphorylation	Any process the stops, prevents, or reduces the frequency, rate or extent of removal of phosphate groups from a protein.
	GO:0042753	positive regulation of circadian rhythm	Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:129 - Pro A:130	[ RasMol ]
		Ala B:129 - Pro B:130	[ RasMol ]

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	KAIA_SYNE7 \| Q79PF6
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UniProtKB/Swiss-Prot
	KAIA_SYNE7 \| Q79PF6	:	1m2e 1m2f 4g86 5c5e 5n8y

1m2e	SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF SYNECHOCOCCUS ELONGATUS KAIA (KAIA135N); AVERAGE MINIMIZED STRUCTURE
1m2f	SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF SYNECHOCOCCUS ELONGATUS KAIA (KAIA135N); FAMILY OF 25 STRUCTURES
1q6a	SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF THERMOSYNECHOCOCCUS ELONGATUS KAIA (THKAIA180C); AVERAGED MINIMIZED STRUCTURE
1q6b	SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF THERMOSYNECHOCOCCUS ELONGATUS KAIA (THKAIA180C); ENSEMBLE OF 25 STRUCTURES

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

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