3R7F - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CP-BOUND ASPARTATE TRANSCARBAMOYLASE FROM BACILLUS SUBTILIS

Authors :   G. M. Cockrell, K. M. Harris, D. E. Puleo, E. R. Kantrowitz

Date :   22 Mar 11 (Deposition) - 08 Jun 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Aspartate Transcarbamoylase, Carbamoyl Phosphate, Transferase, Catalytic Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Harris, G. M. Cockrell, D. E. Puleo, E. R. Kantrowitz
Crystallographic Snapshots Of The Complete Catalytic Cycle Of The Unregulated Aspartate Transcarbamoylase From Bacillu Subtilis.
J. Mol. Biol. V. 411 190 2011
PubMed-ID: 21663747 | Reference-DOI: 10.1016/J.JMB.2011.05.036

Molecule 1 - ASPARTATE CARBAMOYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.1.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PYRB, BSU15490
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	ASPARTATE TRANSCARBAMYLASE, ATCASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 17)

No.	Name	Count	Type	Full Name
1	CP	4	Ligand/Ion	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
2	PO4	13	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:47 , THR A:48 , ARG A:49 , THR A:50 , ARG A:99 , HIS A:127 , GLN A:130 , PRO A:249 , ALA A:250 , HOH A:511 , SER B:74	BINDING SITE FOR RESIDUE CP A 802
02	AC2	SOFTWARE	ASN A:67 , HOH A:438 , HOH A:446 , HOH A:447 , HOH A:478 , HOH A:604 , HOH A:606 , ASN B:67 , ASN C:67 , HOH C:340	BINDING SITE FOR RESIDUE PO4 A 305
03	AC3	SOFTWARE	LYS A:59 , HOH A:317 , HOH A:344 , HOH A:478 , HOH A:497 , HOH A:604 , HOH A:606 , LYS B:59 , LYS C:59	BINDING SITE FOR RESIDUE PO4 A 306
04	AC4	SOFTWARE	SER A:11 , THR A:12 , ARG A:171 , HOH A:418	BINDING SITE FOR RESIDUE PO4 A 307
05	AC5	SOFTWARE	GLN A:23 , LYS A:26 , GLU A:140 , LYS A:272 , HOH A:463	BINDING SITE FOR RESIDUE PO4 A 308
06	AC6	SOFTWARE	LYS A:272 , LYS A:275 , HOH A:406 , HOH A:424 , HOH A:429 , HOH A:468	BINDING SITE FOR RESIDUE PO4 A 309
07	AC7	SOFTWARE	LYS A:241 , ARG A:242 , HIS A:243 , HOH A:379 , HOH A:403	BINDING SITE FOR RESIDUE PO4 A 310
08	AC8	SOFTWARE	SER B:47 , THR B:48 , ARG B:49 , THR B:50 , ARG B:99 , HIS B:127 , GLN B:130 , PRO B:249 , ALA B:250	BINDING SITE FOR RESIDUE CP B 802
09	AC9	SOFTWARE	GLN B:23 , LYS B:26 , GLU B:140 , LYS B:272 , HOH B:380	BINDING SITE FOR RESIDUE PO4 B 305
10	BC1	SOFTWARE	SER B:11 , THR B:12 , ARG B:171 , HOH B:411	BINDING SITE FOR RESIDUE PO4 B 306
11	BC2	SOFTWARE	LYS B:272 , LYS B:275 , HOH B:392 , HOH B:393 , HOH B:414 , HOH B:459	BINDING SITE FOR RESIDUE PO4 B 307
12	BC3	SOFTWARE	HOH A:329 , THR B:144 , PHE B:145 , LYS B:146 , HOH B:350 , HOH B:368 , HOH B:501	BINDING SITE FOR RESIDUE CP B 308
13	BC4	SOFTWARE	SER C:47 , THR C:48 , ARG C:49 , THR C:50 , ARG C:99 , HIS C:127 , GLN C:130 , PRO C:249 , ALA C:250	BINDING SITE FOR RESIDUE CP C 802
14	BC5	SOFTWARE	GLN C:23 , LYS C:26 , GLU C:140 , LYS C:272 , HOH C:572	BINDING SITE FOR RESIDUE PO4 C 305
15	BC6	SOFTWARE	LYS C:272 , LYS C:275 , HOH C:382 , HOH C:383 , HOH C:389 , HOH C:405	BINDING SITE FOR RESIDUE PO4 C 306
16	BC7	SOFTWARE	SER C:11 , THR C:12 , ARG C:171 , HOH C:363 , HOH C:615	BINDING SITE FOR RESIDUE PO4 C 307
17	BC8	SOFTWARE	LYS C:16 , TYR C:139 , THR C:144 , PHE C:145 , LYS C:146 , HOH C:359 , HOH C:621	BINDING SITE FOR RESIDUE PO4 C 308

(no "SS Bond" information available for 3R7F)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:123	-	Cys A:124
2	Ala A:250	-	Pro A:251
3	Ala B:250	-	Pro B:251
4	Ala C:250	-	Pro C:251

(no "SAP(SNP)/Variant" information available for 3R7F)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBAMOYLTRANSFERASE	PS00097	Aspartate and ornithine carbamoyltransferases signature.	PYRB_BACSU	43-50	3	A:43-50 B:43-50 C:43-50

(no "Exon" information available for 3R7F)

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:291
 aligned with PYRB_BACSU | P05654 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:291
                                    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 
           PYRB_BACSU     1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
               SCOP domains d3r7fa1 A:1-143 automated matches                                                                                                              d3r7fa2 A:144-291 automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhh..eeeee.....hhhhhhhhh...eee.......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh..eeeee.hhhhh.......ee.hhhhhhhhh.eeee...............hhhhhhh.hhhhhh......eee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7f A   1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
                                    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

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with PYRB_BACSU | P05654 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:291
                                    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 
           PYRB_BACSU     1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
               SCOP domains d3r7fb1 B:1-143 automated matches                                                                                                              d3r7fb2 B:144-291 automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh..eeeee.hhhhh.......ee.hhhhhhhhh.eeee...............hhhhhhh.hhhhhh......eee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7f B   1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
                                    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

Chain C from PDB  Type:PROTEIN  Length:291
 aligned with PYRB_BACSU | P05654 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:291
                                    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 
           PYRB_BACSU     1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
               SCOP domains d3r7fc1 C:1-143 automated matches                                                                                                              d3r7fc2 C:144-291 automated matches                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -OTCace_N-3r7fC04 C:2-141                                                                                                                    ----OTCace-3r7fC01 C:146-288                                                                                                                       --- Pfam domains (1)
           Pfam domains (2) -OTCace_N-3r7fC05 C:2-141                                                                                                                    ----OTCace-3r7fC02 C:146-288                                                                                                                       --- Pfam domains (2)
           Pfam domains (3) -OTCace_N-3r7fC06 C:2-141                                                                                                                    ----OTCace-3r7fC03 C:146-288                                                                                                                       --- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......ee.hhhhhhhhh.eeee...............hhhhhhh.hhhhhhh.....eee...........hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CARBAMOY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r7f C   1 MKHLTTMSELSTEEIKDLLQTAQELKSGKTDNQLTGKFAANLFFEPSTRTRFSFEVAEKKLGMNVLNLDGTSTSVQKGETLYDTIRTLESIGVDVCVIRHSEDEYYEELVSQVNIPILNAGDGCGQHPTQSLLDLMTIYEEFNTFKGLTVSIHGDIKHSRVARSNAEVLTRLGARVLFSGPSEWQDEENTFGTYVSMDEAVESSDVVMLLRIQNERHQSAVSQEGYLNKYGLTVERAERMKRHAIIMHPAPVNRGVEIDDSLVESEKSRIFKQMKNGVFIRMAVIQRALQT 291
                                    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

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

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: ATC-like (129)

Superfamily: Aspartate/ornithine carbamoyltransferase (122)

Family: automated matches (35)

Protein domain: automated matches (35)

Bacillus subtilis [TaxId: 1423] (3)

1a	d3r7fa1	A:1-143
1b	d3r7fa2	A:144-291
1c	d3r7fb1	B:1-143
1d	d3r7fb2	B:144-291
1e	d3r7fc1	C:1-143
1f	d3r7fc2	C:144-291

(no "CATH Domain" information available for 3R7F)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: OTCace] (48)

Family: OTCace (48)

Bacillus subtilis (3)

1a	OTCace-3r7fC01	C:146-288
1b	OTCace-3r7fC02	C:146-288
1c	OTCace-3r7fC03	C:146-288

Clan: no clan defined [family: OTCace_N] (48)

Family: OTCace_N (48)

Bacillus subtilis (3)

2a	OTCace_N-3r7fC04	C:2-141
2b	OTCace_N-3r7fC05	C:2-141
2c	OTCace_N-3r7fC06	C:2-141

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (PYRB_BACSU | P05654)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0004070	aspartate carbamoyltransferase activity	Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
	GO:0016743	carboxyl- or carbamoyltransferase activity	Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
	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:0044205	'de novo' UMP biosynthetic process	The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0006221	pyrimidine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0000050	urea cycle	The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:250 - Pro A:251	[ RasMol ]
		Ala B:250 - Pro B:251	[ RasMol ]
		Ala C:250 - Pro C:251	[ RasMol ]
		Gly A:123 - Cys A:124	[ RasMol ]

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	3r7f
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	PYRB_BACSU \| P05654	:	2at2 3r7d 3r7l

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 17)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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SCOP Domains (1, 6)

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