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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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI RNA 3' CYCLASE

Authors :   S. Shuman, N. Tanaka, P. Smith

Date :   28 Oct 09 (Deposition) - 21 Apr 10 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

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 :   Cyclase, Rna Processing, 3' Modifying Enzymes, Adenylate, Phosphoramidate, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Tanaka, P. Smith, S. Shuman
Structure Of The Rna 3'-Phosphate Cyclase-Adenylate Intermediate Illuminates Nucleotide Specificity And Covalen Nucleotidyl Transfer.
Structure V. 18 449 2010
PubMed-ID: 20399182 | Reference-DOI: 10.1016/J.STR.2010.01.016

Molecule 1 - RNA 3'-TERMINAL PHOSPHATE CYCLASE
	Chains	:	A, B, C, D
	EC Number	:	6.5.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)-CODONPLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B4475, JW5688, RTCA, YHGJ, YHGK, YP_026219
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	511145
	Strain	:	K-12 SUBSTR. MG1655
	Synonym	:	RNA-3'-PHOSPHATE CYCLASE, RNA CYCLASE

		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 (4, 27)

No.	Name	Count	Type	Full Name
1	AMP	4	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	10	Ligand/Ion	GLYCEROL
3	NA	5	Ligand/Ion	SODIUM ION
4	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	3	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 5)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	3	Ligand/Ion	GLYCEROL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:18 , ARG A:21 , GLN A:104 , SER A:129 , ALA A:130 , PRO A:131 , PHE A:251 , TYR A:284 , ASP A:287 , GLN A:288 , HIS A:309 , HOH A:367 , HOH A:374 , HOH A:386 , HOH A:397 , HOH A:439 , HOH A:710 , HOH A:1423 , HOH A:1432	BINDING SITE FOR RESIDUE AMP A 501
02	AC2	SOFTWARE	GLY A:16 , GLY A:17 , ARG A:21 , GLN A:51 , ALA A:55 , ILE A:93 , VAL A:102 , HOH A:457 , HOH A:677	BINDING SITE FOR RESIDUE GOL A 340
03	AC3	SOFTWARE	ASP A:88 , PRO A:116 , SER A:117 , GLU A:171 , HOH A:396 , ARG C:4	BINDING SITE FOR RESIDUE GOL A 341
04	AC4	SOFTWARE	GLY A:17 , SO4 A:344 , HOH A:471	BINDING SITE FOR RESIDUE NA A 342
05	AC5	SOFTWARE	GLU A:14 , ARG A:43 , HOH A:429 , HOH A:471 , HOH A:542 , HOH A:918	BINDING SITE FOR RESIDUE SO4 A 343
06	AC6	SOFTWARE	GLN A:51 , HIS A:52 , NA A:342 , HOH A:399 , HOH A:429 , HOH A:677 , HOH A:832	BINDING SITE FOR RESIDUE SO4 A 344
07	AC7	SOFTWARE	SER A:218 , HIS A:220 , HOH A:972 , HOH A:1412 , PRO B:228 , ARG B:229 , HOH B:1074	BINDING SITE FOR RESIDUE SO4 A 345
08	AC8	SOFTWARE	GLN B:18 , ARG B:21 , GLN B:104 , SER B:129 , ALA B:130 , PRO B:131 , PHE B:251 , TYR B:284 , ASP B:287 , GLN B:288 , HIS B:309 , HOH B:367 , HOH B:409 , HOH B:422 , HOH B:446 , HOH B:949 , HOH B:1327	BINDING SITE FOR RESIDUE AMP B 501
09	AC9	SOFTWARE	PHE B:112 , LEU B:295 , HOH B:1311 , HOH B:1438 , HOH B:1491	BINDING SITE FOR RESIDUE GOL B 340
10	BC1	SOFTWARE	HIS B:-12 , ARG B:85 , HOH B:1266	BINDING SITE FOR RESIDUE GOL B 341
11	BC2	SOFTWARE	ARG B:40 , SO4 B:343 , HOH B:473	BINDING SITE FOR RESIDUE NA B 342
12	BC3	SOFTWARE	GLU B:14 , ARG B:40 , ARG B:43 , NA B:342 , HOH B:475 , HOH B:835 , HOH B:871 , HOH B:1256	BINDING SITE FOR RESIDUE SO4 B 343
13	BC4	SOFTWARE	ARG B:208 , SER B:259 , ALA B:260 , HOH B:1140	BINDING SITE FOR RESIDUE SO4 B 344
14	BC5	SOFTWARE	GLN C:18 , ARG C:21 , GLN C:104 , SER C:129 , ALA C:130 , PRO C:131 , PHE C:251 , TYR C:284 , ASP C:287 , GLN C:288 , HIS C:309 , HOH C:384 , HOH C:394 , HOH C:401 , HOH C:402 , HOH C:481 , HOH C:621 , HOH C:920 , HOH C:1428	BINDING SITE FOR RESIDUE AMP C 501
15	BC6	SOFTWARE	ASP A:114 , GLU C:318 , ARG C:324 , PHE C:325 , GLY D:200	BINDING SITE FOR RESIDUE GOL C 340
16	BC7	SOFTWARE	HOH B:990 , MET C:5 , LEU C:78 , ARG C:80 , HOH C:1273	BINDING SITE FOR RESIDUE GOL C 341
17	BC8	SOFTWARE	GLY C:16 , ARG C:21 , GLN C:51 , HIS C:52 , ALA C:55 , ILE C:93 , LEU C:101 , VAL C:102 , SO4 C:346 , HOH C:784 , HOH C:1171 , HOH C:1507	BINDING SITE FOR RESIDUE GOL C 342
18	BC9	SOFTWARE	LEU C:275 , ALA C:276 , SER C:277 , HOH C:442	BINDING SITE FOR RESIDUE NA C 343
19	CC1	SOFTWARE	ARG C:40 , SO4 C:345 , HOH C:367 , HOH C:1026	BINDING SITE FOR RESIDUE NA C 344
20	CC2	SOFTWARE	GLU C:14 , ARG C:40 , ARG C:43 , NA C:344 , HOH C:370 , HOH C:715 , HOH C:1178 , HOH C:1211	BINDING SITE FOR RESIDUE SO4 C 345
21	CC3	SOFTWARE	GLN C:51 , HIS C:52 , GOL C:342 , HOH C:819 , HOH C:1178 , HOH C:1268 , HOH C:1405 , HOH C:1507	BINDING SITE FOR RESIDUE SO4 C 346
22	CC4	SOFTWARE	ARG D:21 , GLN D:104 , SER D:129 , ALA D:130 , PRO D:131 , PHE D:251 , TYR D:284 , ASP D:287 , GLN D:288 , HIS D:309 , HOH D:363 , HOH D:413 , HOH D:431 , HOH D:528	BINDING SITE FOR RESIDUE AMP D 501
23	CC5	SOFTWARE	LYS D:3 , ARG D:4 , MET D:5	BINDING SITE FOR RESIDUE GOL D 340
24	CC6	SOFTWARE	HIS D:204 , VAL D:205 , ARG D:208 , GLU D:261	BINDING SITE FOR RESIDUE GOL D 341
25	CC7	SOFTWARE	GLY D:64 , ALA D:65 , THR D:66 , ARG D:80 , PRO D:81	BINDING SITE FOR RESIDUE GOL D 342
26	CC8	SOFTWARE	ARG D:40 , SO4 D:344 , HOH D:1378	BINDING SITE FOR RESIDUE NA D 343
27	CC9	SOFTWARE	GLU D:14 , ARG D:40 , ARG D:43 , NA D:343 , HOH D:358 , HOH D:981 , HOH D:1126	BINDING SITE FOR RESIDUE SO4 D 344

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

Asymmetric Unit

No.	Residues
1	Tyr A:161	-	Pro A:162
2	Gly A:232	-	Pro A:233
3	Tyr B:161	-	Pro B:162
4	Gly B:232	-	Pro B:233
5	Tyr C:161	-	Pro C:162
6	Gly C:232	-	Pro C:233
7	Tyr D:161	-	Pro D:162
8	Gly D:232	-	Pro D:233

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	4	A:158-168 B:158-168 C:158-168 D:158-168

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	1	A:158-168 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	1	- B:158-168 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	1	- - C:158-168 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RTC	PS01287	RNA 3'-terminal phosphate cyclase signature.	RTCA_ECOLI	157-167	1	- - - D:158-168

(no "Exon" information available for 3KGD)

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:336
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:336
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332      
           RTCA_ECOLI     3 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3kgdA01 A:4-182,A:277-337  [code=3.65.10.20, no name defined]                                                                                                                      ---3kgdA02 A:186-276  [code=3.30.360.20, no name defined]                                     3kgdA01 A:4-182,A:277-337  [code=3.65.10.20, no name defined]-- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeeeeeeeeehhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee................eeeeeeeeeee..hhhhhhhhhhhhhh.....eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kgd A   4 RMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:342
                                1                                                                                                                                                                                                                                                                                                                                                 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336  
           RTCA_ECOLI     - ----MKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3kgdB01 B:-13-182,B:277-337  [code=3.65.10.20, no name defined]                                                                                                                          ---3kgdB02 B:186-276  [code=3.30.360.20, no name defined]                                     3kgdB01 B:-13-182,B:277-337                                  -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeee.....hhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeee.......ee......eeeeeeeeeee..hhhhhhhhhhhhhh.....eeeeee.......eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kgd B -13 HHHHHKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                ||   7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337  
                               -9|                                                                                                                                                                                                                                                                                                                                                
                                 3

Chain C from PDB  Type:PROTEIN  Length:338
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:338
                                    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       290       300       310       320       330        
           RTCA_ECOLI     1 MKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3kgdC01 C:2-182,C:277-337  [code=3.65.10.20, no name defined]                                                                                                                        ---3kgdC02 C:186-276  [code=3.30.360.20, no name defined]                                     3kgdC01 C:2-182,C:277-337  [code=3.65.10.20, no name defined]-- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeeeeeeeeehhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee................eeeeeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeehhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kgd C   2 MKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain D from PDB  Type:PROTEIN  Length:340
 aligned with RTCA_ECOLI | P46849 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:340
                              1                                                                                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
           RTCA_ECOLI     - --MKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 338
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3kgdD01 D:0-182,D:277-337  [code=3.65.10.20, no name defined]                                                                                                                          ---3kgdD02 D:186-276  [code=3.30.360.20, no name defined]                                     3kgdD01 D:0-182,D:277-337  [code=3.65.10.20, no name defined]-- CATH domains
           Pfam domains (1) --------RTC-3kgdD01 D:8-329                                                                                                                                                                                                                                                                                                               ---------- Pfam domains (1)
           Pfam domains (2) --------RTC-3kgdD02 D:8-329                                                                                                                                                                                                                                                                                                               ---------- Pfam domains (2)
           Pfam domains (3) --------RTC-3kgdD03 D:8-329                                                                                                                                                                                                                                                                                                               ---------- Pfam domains (3)
           Pfam domains (4) --------RTC-3kgdD04 D:8-329                                                                                                                                                                                                                                                                                                               ---------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RTC_insert-3kgdD05 D:184-278                                                                   ------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RTC_insert-3kgdD06 D:184-278                                                                   ------------------------------------------------------------- Pfam domains (6)
           Pfam domains (7) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RTC_insert-3kgdD07 D:184-278                                                                   ------------------------------------------------------------- Pfam domains (7)
           Pfam domains (8) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RTC_insert-3kgdD08 D:184-278                                                                   ------------------------------------------------------------- Pfam domains (8)
         Sec.struct. author ......eeee.......hhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhhh.eee........eeee.......eeeee.....hhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee................eeeeeeeeeee...hhhhhhhhhhhhhhh...eeeeee.hhhhh.eeeeeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------RTC        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kgd D   0 RHMKRMIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGTDNPSAPPADFIRRVLEPLLAKIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNTLQLGERGNIVQMRGEVLLAGVPRHVAEREIATLAGSFSLHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQLVLPMALAGAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIETDGVTRVSIE 339
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

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 3KGD)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dihydrodipicolinate Reductase; domain 2 (182)

Homologous Superfamily: [code=3.30.360.20, no name defined] (3)

K-12 substr (Escherichia coli str) (1)

1a	3kgdA02	A:186-276
1b	3kgdB02	B:186-276
1c	3kgdC02	C:186-276
1d	3kgdD02	D:186-276

Architecture: Alpha-beta prism (50)

Topology: UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain (50)

Homologous Superfamily: [code=3.65.10.20, no name defined] (3)

K-12 substr (Escherichia coli str) (1)

2a	3kgdA01	A:4-182,A:277-337
2b	3kgdC01	C:2-182,C:277-337
2c	3kgdD01	D:0-182,D:277-337
2d	3kgdB01	B:-13-182,B:277-337

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EPT_RTPC (43)

Family: RTC (3)

Escherichia coli (strain K12) (2)

1a	RTC-3kgdD01	D:8-329
1b	RTC-3kgdD02	D:8-329
1c	RTC-3kgdD03	D:8-329
1d	RTC-3kgdD04	D:8-329

Clan: no clan defined [family: RTC_insert] (3)

Family: RTC_insert (3)

Escherichia coli (strain K12) (2)

2a	RTC_insert-3kgdD05	D:184-278
2b	RTC_insert-3kgdD06	D:184-278
2c	RTC_insert-3kgdD07	D:184-278
2d	RTC_insert-3kgdD08	D:184-278

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RTCA_ECOLI | P46849)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003963	RNA-3'-phosphate cyclase activity	Catalysis of the reaction: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
cellular component
	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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	3kgd
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	RTCA_ECOLI \| P46849	:	1qmh 1qmi 3tut 3tux 3tv1 3tw3

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 27)

Sites (27, 27)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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Exons (0, 0)

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