4LCQ - JenaLib

Title :   THE CRYSTAL STRUCTURE OF DI-ZN DIHYDROPYRIMIDINASE IN COMPLEX WITH NCBI

Authors :   Y. C. Hsieh, M. C. Chen, C. C. Hsu, S. I. Chan, Y. S. Yang, C. J. Chen

Date :   22 Jun 13 (Deposition) - 18 Sep 13 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.81

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Hydrolase, Zinc Binding, Carboxylation, Alpha-Beta Barrel, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. C. Hsieh, M. C. Chen, C. C. Hsu, S. I. Chan, Y. S. Yang, C. J. Chen
Crystal Structures Of Vertebrate Dihydropyrimidinase And Complexes From Tetraodon Nigroviridis With Lysine Carbamylation: Metal And Structural Requirements For Post-Translational Modification And Function.
J. Biol. Chem. V. 288 30645 2013
PubMed-ID: 24005677 | Reference-DOI: 10.1074/JBC.M113.496778

Compounds

Molecule 1 - DIHYDROPYRIMIDINASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET44A(+)
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SPOTTED GREEN PUFFERFISH
	Organism Scientific	:	TETRAODON NIGROVIRIDIS
	Organism Taxid	:	99883

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	URQ	1	Ligand/Ion	(2S)-3-(CARBAMOYLAMINO)-2-METHYLPROPANOIC ACID
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	KCX	4	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	URQ	4	Ligand/Ion	(2S)-3-(CARBAMOYLAMINO)-2-METHYLPROPANOIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:63 , HIS A:65 , KCX A:155 , ASP A:322 , ZN A:602 , URQ A:603	BINDING SITE FOR RESIDUE ZN A 601
2	AC2	SOFTWARE	KCX A:155 , HIS A:188 , HIS A:244 , ZN A:601 , URQ A:603	BINDING SITE FOR RESIDUE ZN A 602
3	AC3	SOFTWARE	HIS A:65 , KCX A:155 , TYR A:160 , HIS A:188 , HIS A:244 , MET A:293 , GLY A:294 , ASP A:322 , ASN A:343 , ZN A:601 , ZN A:602	BINDING SITE FOR RESIDUE URQ A 603

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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

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Chain A from PDB  Type:PROTEIN  Length:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eee.eeeee..eeeeee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhh.............hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...............eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lcq A   4 AGEILIKGGKVVNEDCSFFSDVHIRGGKIVEVGPDLRVPPGARVIDATDRLVIPGGIDTHTHMELAFMGTRAVDDFHIGTKAALAGGTTMILDFVMTQKGQSLLEAYDLWRKTADPKVCCDYSLHVAVTWWSDEVKDEMRTLAQERGVNSFkMFMAYKGLFMLRDDELYAVFSHCKEVGAIAQVHAENGDLIAEGAKKMLSLGITGPEGHELCRPEAVEAEATQRAITIASAVNCPLYVVHVMSKSAADVVSKARKDGRVVFGEPIAASLGTDGTNYWHKDWAHAAQYVMGPPLRPDPSTPGYLMDLLANDDLTLTGTDNCTFSRCQKALGKDDFTRIPNGVNGVEDRMSVIWEKGVHSGKMDENRFVAVTSSNAAKIFNFYPQKGRIAKDSDADVVIWDPKTTRKISAQTHHQAVDYNIFEGMECHGVPVVTVSRGRVVYEEGRLKVSPGQGRFIHRQPFSEFVYKRIRQRDEVGKPAVVIREP 488
                                    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       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483     
                                                                                                                                                                                 155-KCX

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	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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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	Ligands, Modified Residues, Ions
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		URQ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
		Gly A:294 - Pro A:295	[ RasMol ]
		Tyr A:385 - Pro A:386	[ RasMol ]

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